Starting phenix.real_space_refine on Mon Mar 25 09:12:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyb_8136/03_2024/5iyb_8136.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyb_8136/03_2024/5iyb_8136.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/5iyb_8136/03_2024/5iyb_8136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyb_8136/03_2024/5iyb_8136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyb_8136/03_2024/5iyb_8136.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyb_8136/03_2024/5iyb_8136.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 148 5.49 5 Mg 2 5.21 5 S 270 5.16 5 C 29597 2.51 5 N 8401 2.21 5 O 9299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B GLU 765": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B GLU 879": "OE1" <-> "OE2" Residue "B GLU 881": "OE1" <-> "OE2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B ARG 897": "NH1" <-> "NH2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "K GLU 85": "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 248": "NH1" <-> "NH2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "N GLU 317": "OE1" <-> "OE2" Residue "N GLU 327": "OE1" <-> "OE2" Residue "N ARG 363": "NH1" <-> "NH2" 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 GLU 326": "OE1" <-> "OE2" Residue "P ARG 336": "NH1" <-> "NH2" Residue "Q PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 172": "OE1" <-> "OE2" Residue "S ARG 180": "NH1" <-> "NH2" Residue "T ARG 177": "NH1" <-> "NH2" Residue "T GLU 234": "OE1" <-> "OE2" Residue "U GLU 146": "OE1" <-> "OE2" Residue "U GLU 227": "OE1" <-> "OE2" Residue "U GLU 243": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 47728 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: {'PTRANS': 7, 'TRANS': 214} 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: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1553 Classifications: {'DNA': 75} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 74} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1517 Classifications: {'DNA': 75} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 74} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 52.598 116.820 105.520 1.00 0.00 S ATOM 494 SG CYS A 74 51.974 121.066 106.273 1.00 0.00 S ATOM 541 SG CYS A 81 53.942 118.714 103.099 1.00 0.00 S ATOM 776 SG CYS A 111 100.484 118.895 113.975 1.00 0.00 S ATOM 804 SG CYS A 114 99.926 120.260 117.992 1.00 0.00 S ATOM 1117 SG CYS A 154 103.008 120.809 115.531 1.00 0.00 S ATOM 1162 SG CYS A 184 102.211 116.774 116.746 1.00 0.00 S ATOM 20402 SG CYS B1119 62.748 130.355 113.267 1.00 0.00 S ATOM 20424 SG CYS B1122 65.849 127.935 111.711 1.00 0.00 S ATOM 20539 SG CYS B1137 61.983 126.719 113.599 1.00 0.00 S ATOM 20560 SG CYS B1140 65.599 127.647 115.367 1.00 0.00 S ATOM 21535 SG CYS C 88 10.437 127.953 52.106 1.00 0.00 S ATOM 21548 SG CYS C 90 12.136 124.806 54.299 1.00 0.00 S ATOM 21583 SG CYS C 94 10.188 124.123 51.055 1.00 0.00 S ATOM 21605 SG CYS C 97 13.814 125.378 50.947 1.00 0.00 S ATOM 29208 SG CYS I 17 130.562 91.636 62.151 1.00 0.00 S ATOM 29232 SG CYS I 20 128.237 90.207 64.687 1.00 0.00 S ATOM 29393 SG CYS I 39 128.702 93.455 65.788 1.00 0.00 S ATOM 29418 SG CYS I 42 131.719 91.144 65.937 1.00 0.00 S ATOM 29770 SG CYS I 86 114.261 110.119 24.082 1.00 0.00 S ATOM 29794 SG CYS I 89 112.865 107.795 21.012 1.00 0.00 S ATOM 29998 SG CYS I 114 111.032 107.562 24.242 1.00 0.00 S ATOM 30033 SG CYS I 119 114.967 106.465 23.775 1.00 0.00 S ATOM 30143 SG CYS J 7 41.305 123.873 34.496 1.00 0.00 S ATOM 30167 SG CYS J 10 38.733 126.032 33.058 1.00 0.00 S ATOM 30431 SG CYS J 44 42.436 126.648 31.692 1.00 0.00 S ATOM 30437 SG CYS J 45 40.130 124.420 30.370 1.00 0.00 S ATOM 31616 SG CYS L 19 36.183 87.360 57.178 1.00 0.00 S ATOM 31635 SG CYS L 22 34.006 85.448 55.561 1.00 0.00 S ATOM 31752 SG CYS L 36 34.374 84.926 59.580 1.00 0.00 S ATOM 31778 SG CYS L 39 37.992 84.237 56.578 1.00 0.00 S ATOM 32013 SG CYS M 15 29.935 122.613 96.296 1.00 0.00 S ATOM 32160 SG CYS M 34 29.547 121.129 92.649 1.00 0.00 S ATOM 32182 SG CYS M 37 28.717 125.121 93.226 1.00 0.00 S ATOM 38417 SG CYS Q 129 36.202 112.008 127.754 1.00 0.00 S ATOM 38437 SG CYS Q 132 39.059 111.555 125.209 1.00 0.00 S ATOM 38609 SG CYS Q 154 37.058 114.995 125.278 1.00 0.00 S ATOM 38633 SG CYS Q 157 35.542 111.839 123.821 1.00 0.00 S ATOM 44342 SG CYS U 263 87.926 158.161 49.557 1.00 0.00 S ATOM 44361 SG CYS U 266 91.699 159.210 49.270 1.00 0.00 S ATOM 44559 SG CYS U 291 90.408 155.449 49.953 1.00 0.00 S ATOM 44582 SG CYS U 294 90.343 158.018 52.354 1.00 0.00 S Time building chain proxies: 23.60, per 1000 atoms: 0.49 Number of scatterers: 47728 At special positions: 0 Unit cell: (184.71, 213.53, 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 148 15.00 Mg 2 11.99 O 9299 8.00 N 8401 7.00 C 29597 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: 20.58 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " 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 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " 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 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " 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 402 " pdb="ZN ZN U 402 " - pdb=" SG CYS U 294 " pdb="ZN ZN U 402 " - pdb=" SG CYS U 291 " pdb="ZN ZN U 402 " - pdb=" SG CYS U 266 " pdb="ZN ZN U 402 " - 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: 214 helices and 48 sheets defined 41.2% alpha, 16.6% beta 52 base pairs and 118 stacking pairs defined. Time for finding SS restraints: 15.86 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 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.750A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 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 344 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 408 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.630A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 518 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.622A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.852A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 removed outlier: 3.637A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.650A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.638A 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 660 Processing helix chain 'A' and resid 661 through 684 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 Processing helix chain 'A' and resid 817 through 820 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.788A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.596A 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 938 through 943 removed outlier: 3.596A pdb=" N VAL A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.510A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1037 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: 3.566A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1100 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.601A pdb=" N VAL A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) 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 1264 through 1268 removed outlier: 3.825A pdb=" N ASN A1267 " --> pdb=" O SER A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1296 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1362 through 1370 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.655A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.975A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.775A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 Processing helix chain 'A' and resid 1453 through 1461 removed outlier: 3.646A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1471 removed outlier: 4.110A pdb=" N PHE A1471 " --> pdb=" O THR A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1484 removed outlier: 3.515A pdb=" N MET A1484 " --> pdb=" O CYS A1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 24 No H-bonds generated for 'chain 'B' and resid 22 through 24' Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.986A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.788A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.666A pdb=" N GLY B 165 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 290 removed outlier: 3.769A pdb=" N TYR B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 309 Proline residue: B 303 - end of helix removed outlier: 3.637A pdb=" N PHE B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 331 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 377 removed outlier: 3.509A pdb=" N ALA B 362 " --> pdb=" O GLU B 358 " (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: 3.611A pdb=" N ASN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.245A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 removed outlier: 3.509A pdb=" N ARG B 463 " --> pdb=" O HIS B 460 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 464 " --> pdb=" O GLN B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 464' Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 549 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 Processing helix chain 'B' and resid 607 through 609 No H-bonds generated for 'chain 'B' and resid 607 through 609' Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.586A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 648 No H-bonds generated for 'chain 'B' and resid 646 through 648' Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.611A pdb=" N MET B 702 " --> pdb=" O HIS B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.619A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 711 " --> pdb=" O CYS B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 706 through 711' Processing helix chain 'B' and resid 713 through 718 removed outlier: 5.626A pdb=" N GLN B 718 " --> pdb=" O ASP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 732 removed outlier: 3.757A pdb=" N THR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 removed outlier: 4.568A pdb=" N HIS B 741 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 767 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.552A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 994 Processing helix chain 'B' and resid 1006 through 1018 Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.775A 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 removed outlier: 3.668A pdb=" N GLN B1094 " --> pdb=" O GLU B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1107 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.655A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.631A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 267 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 33 through 50 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 120 removed outlier: 3.948A pdb=" N GLY D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.931A pdb=" N LEU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 4.051A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 36 through 44 removed outlier: 3.619A pdb=" N ALA E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.594A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 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 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 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 128 through 132 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 28 Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.683A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.305A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 Processing helix chain 'M' and resid 27 through 30 Processing helix chain 'M' and resid 47 through 55 removed outlier: 4.193A pdb=" N TRP M 52 " --> pdb=" O GLY M 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE M 55 " --> pdb=" O TRP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 76 removed outlier: 3.832A pdb=" N LEU M 75 " --> pdb=" O ASN M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 111 through 128 removed outlier: 3.564A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.848A pdb=" N VAL M 135 " --> pdb=" O PRO M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 184 Processing helix chain 'M' and resid 187 through 202 Processing helix chain 'M' and resid 211 through 222 removed outlier: 3.702A pdb=" N MET M 215 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 243 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 294 through 300 Proline residue: M 297 - end of helix removed outlier: 3.753A pdb=" N PHE M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 294 through 300' Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'N' and resid 10 through 33 removed outlier: 4.670A pdb=" N ASP N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE N 28 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 51 removed outlier: 3.766A pdb=" N LEU N 39 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 314 through 318 removed outlier: 3.697A pdb=" N ASP N 318 " --> pdb=" O ASN N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 330 removed outlier: 4.273A pdb=" N PHE N 329 " --> pdb=" O GLY N 325 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP N 330 " --> pdb=" O GLN N 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 325 through 330' Processing helix chain 'O' and resid 4 through 8 Processing helix chain 'O' and resid 9 through 25 Processing helix chain 'O' and resid 29 through 52 Processing helix chain 'P' and resid 179 through 187 Processing helix chain 'P' and resid 226 through 245 Processing helix chain 'P' and resid 269 through 277 removed outlier: 3.613A pdb=" N LEU P 273 " --> pdb=" O ARG P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 334 removed outlier: 3.831A 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 39 removed outlier: 3.817A pdb=" N ARG Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 53 Processing helix chain 'Q' and resid 55 through 69 removed outlier: 3.518A pdb=" N ASP Q 69 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'Q' and resid 137 through 142 removed outlier: 3.820A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 201 Proline residue: Q 186 - end of helix removed outlier: 4.013A pdb=" N LEU Q 190 " --> pdb=" O PRO Q 186 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU Q 191 " --> pdb=" O ILE Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'R' and resid 76 through 92 Processing helix chain 'R' and resid 98 through 107 Processing helix chain 'R' and resid 108 through 111 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'R' and resid 122 through 127 Processing helix chain 'R' and resid 146 through 150 Processing helix chain 'R' and resid 151 through 157 Processing helix chain 'R' and resid 167 through 174 removed outlier: 3.844A pdb=" N ALA R 174 " --> pdb=" O ASP R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 185 removed outlier: 4.729A pdb=" N LYS R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 223 removed outlier: 3.938A pdb=" N VAL R 223 " --> pdb=" O LEU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'S' and resid 5 through 9 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 160 through 167 Processing helix chain 'S' and resid 173 through 179 removed outlier: 4.062A pdb=" N MET S 177 " --> pdb=" O HIS S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 14 Processing helix chain 'T' and resid 25 through 35 Processing helix chain 'T' and resid 122 through 137 removed outlier: 4.112A pdb=" N ARG T 126 " --> pdb=" O GLU T 122 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU T 127 " --> pdb=" O ASN T 123 " (cutoff:3.500A) removed outlier: 3.609A 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 180 through 192 Processing helix chain 'T' and resid 199 through 207 Processing helix chain 'T' and resid 209 through 220 removed outlier: 4.176A pdb=" N LEU T 213 " --> pdb=" O PRO T 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 153 Processing helix chain 'U' and resid 156 through 162 removed outlier: 4.098A pdb=" N ALA U 160 " --> pdb=" O ASP U 156 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE U 161 " --> pdb=" O ASP U 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 181 removed outlier: 3.571A pdb=" N GLU U 179 " --> pdb=" O ALA U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 199 Processing helix chain 'U' and resid 203 through 212 removed outlier: 4.242A 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 233 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.850A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.147A pdb=" N ILE A 249 " --> 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 'B' and resid 1060 through 1062 removed outlier: 3.529A pdb=" N SER A 362 " --> pdb=" O ARG B1062 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.130A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.522A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.786A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB1, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB2, first strand: chain 'A' and resid 1308 through 1312 Processing sheet with id=AB3, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 4.075A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1472 through 1475 removed outlier: 3.570A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.822A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.277A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 205 through 209 removed outlier: 3.513A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC2, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC3, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.498A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.053A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 943 through 944 removed outlier: 4.490A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 794 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 949 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET B 796 " --> pdb=" O TYR B 949 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 943 through 944 Processing sheet with id=AC7, first strand: chain 'B' and resid 826 through 829 removed outlier: 6.609A pdb=" N GLN B 838 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1114 through 1119 Processing sheet with id=AC9, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.487A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.742A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 113 through 115 removed outlier: 4.013A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.764A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.764A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.642A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.517A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN G 91 " --> pdb=" O PHE G 98 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP G 141 " --> pdb=" O VAL G 89 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AD9, first strand: chain 'I' and resid 25 through 29 removed outlier: 3.730A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.939A pdb=" N ALA I 94 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE3, first strand: chain 'M' and resid 24 through 25 Processing sheet with id=AE4, first strand: chain 'N' and resid 363 through 366 removed outlier: 3.793A pdb=" N ARG N 363 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS N 369 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE O 58 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE N 371 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N GLY O 60 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP N 373 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU O 62 " --> pdb=" O ASP N 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU N 375 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR O 64 " --> pdb=" O GLU N 375 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE O 58 " --> pdb=" O PHE O 81 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE O 81 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY O 60 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL O 79 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU O 62 " --> pdb=" O ASN O 77 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASN O 77 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP O 91 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU O 80 " --> pdb=" O LYS O 89 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS O 89 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG O 82 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU O 87 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN N 333 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ASN N 333 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU N 360 " --> pdb=" O ASN N 333 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL N 335 " --> pdb=" O MET N 358 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET N 358 " --> pdb=" O VAL N 335 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS N 337 " --> pdb=" O GLY N 356 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLY N 356 " --> pdb=" O CYS N 337 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR N 339 " --> pdb=" O LYS N 354 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS N 354 " --> pdb=" O TYR N 339 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 190 through 191 removed outlier: 5.101A pdb=" N LEU P 165 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER P 261 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR P 171 " --> pdb=" O ILE P 255 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE P 255 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ASN P 173 " --> pdb=" O PHE P 253 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE P 253 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 72 through 76 Processing sheet with id=AE7, first strand: chain 'Q' and resid 127 through 128 Processing sheet with id=AE8, first strand: chain 'R' and resid 131 through 133 Processing sheet with id=AE9, first strand: chain 'R' and resid 165 through 166 Processing sheet with id=AF1, first strand: chain 'S' and resid 45 through 49 removed outlier: 3.608A pdb=" N ASN S 142 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA S 30 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASN S 32 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE T 96 " --> pdb=" O ASN S 27 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N GLN T 91 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLN T 112 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU T 93 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY T 41 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA S 134 " --> pdb=" O CYS S 130 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL T 18 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ALA T 114 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU T 20 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N CYS T 116 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS T 22 " --> pdb=" O CYS T 116 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 197 through 198 Processing sheet with id=AF3, first strand: chain 'U' and resid 272 through 274 1927 hydrogen bonds defined for protein. 5316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 138 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 118 stacking parallelities Total time for adding SS restraints: 25.84 Time building geometry restraints manager: 21.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 7778 1.29 - 1.44: 13013 1.44 - 1.58: 27378 1.58 - 1.72: 313 1.72 - 1.86: 426 Bond restraints: 48908 Sorted by residual: bond pdb=" CA ILE B 947 " pdb=" CB ILE B 947 " ideal model delta sigma weight residual 1.553 1.505 0.048 7.40e-03 1.83e+04 4.20e+01 bond pdb=" CA VAL B 794 " pdb=" CB VAL B 794 " ideal model delta sigma weight residual 1.544 1.626 -0.082 1.38e-02 5.25e+03 3.50e+01 bond pdb=" CA VAL B 801 " pdb=" CB VAL B 801 " ideal model delta sigma weight residual 1.540 1.614 -0.073 1.25e-02 6.40e+03 3.44e+01 bond pdb=" C VAL A 474 " pdb=" O VAL A 474 " ideal model delta sigma weight residual 1.234 1.152 0.082 1.43e-02 4.89e+03 3.29e+01 bond pdb=" CA TYR B 811 " pdb=" C TYR B 811 " ideal model delta sigma weight residual 1.520 1.459 0.061 1.21e-02 6.83e+03 2.55e+01 ... (remaining 48903 not shown) Histogram of bond angle deviations from ideal: 64.71 - 79.75: 4 79.75 - 94.80: 13 94.80 - 109.84: 10030 109.84 - 124.89: 55330 124.89 - 139.93: 1296 Bond angle restraints: 66673 Sorted by residual: angle pdb=" N LYS A1115 " pdb=" CA LYS A1115 " pdb=" C LYS A1115 " ideal model delta sigma weight residual 111.30 81.74 29.56 1.43e+00 4.89e-01 4.27e+02 angle pdb=" N ALA M 91 " pdb=" CA ALA M 91 " pdb=" C ALA M 91 " ideal model delta sigma weight residual 112.12 90.67 21.45 1.34e+00 5.57e-01 2.56e+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 64.71 60.29 4.10e+00 5.95e-02 2.16e+02 angle pdb=" N GLU I 61 " pdb=" CA GLU I 61 " pdb=" C GLU I 61 " ideal model delta sigma weight residual 109.62 89.02 20.60 1.50e+00 4.44e-01 1.89e+02 angle pdb=" C GLU P 206 " pdb=" N PRO P 207 " pdb=" CD PRO P 207 " ideal model delta sigma weight residual 125.00 70.96 54.04 4.10e+00 5.95e-02 1.74e+02 ... (remaining 66668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 28254 34.81 - 69.62: 1231 69.62 - 104.43: 95 104.43 - 139.25: 3 139.25 - 174.06: 3 Dihedral angle restraints: 29586 sinusoidal: 13327 harmonic: 16259 Sorted by residual: dihedral pdb=" CA GLU N 324 " pdb=" C GLU N 324 " pdb=" N GLY N 325 " pdb=" CA GLY N 325 " ideal model delta harmonic sigma weight residual 180.00 76.73 103.27 0 5.00e+00 4.00e-02 4.27e+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 -124.37 -55.63 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA ASP N 355 " pdb=" C ASP N 355 " pdb=" N GLY N 356 " pdb=" CA GLY N 356 " ideal model delta harmonic sigma weight residual 180.00 -131.23 -48.77 0 5.00e+00 4.00e-02 9.52e+01 ... (remaining 29583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 7153 0.160 - 0.320: 224 0.320 - 0.481: 27 0.481 - 0.641: 7 0.641 - 0.801: 5 Chirality restraints: 7416 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 1.71 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA GLN U 257 " pdb=" N GLN U 257 " pdb=" C GLN U 257 " pdb=" CB GLN U 257 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA GLU B 79 " pdb=" N GLU B 79 " pdb=" C GLU B 79 " pdb=" CB GLU B 79 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 7413 not shown) Planarity restraints: 8144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU P 206 " 0.167 5.00e-02 4.00e+02 2.47e-01 9.75e+01 pdb=" N PRO P 207 " -0.422 5.00e-02 4.00e+02 pdb=" CA PRO P 207 " 0.181 5.00e-02 4.00e+02 pdb=" CD PRO P 207 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 261 " -0.160 5.00e-02 4.00e+02 2.42e-01 9.35e+01 pdb=" N PRO A 262 " 0.414 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " -0.175 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 194 " -0.159 5.00e-02 4.00e+02 2.41e-01 9.30e+01 pdb=" N PRO R 195 " 0.413 5.00e-02 4.00e+02 pdb=" CA PRO R 195 " -0.174 5.00e-02 4.00e+02 pdb=" CD PRO R 195 " -0.080 5.00e-02 4.00e+02 ... (remaining 8141 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 37 1.87 - 2.63: 1107 2.63 - 3.39: 63605 3.39 - 4.14: 115102 4.14 - 4.90: 200997 Nonbonded interactions: 380848 Sorted by model distance: nonbonded pdb=" CG LEU E 27 " pdb=" CD2 HIS E 64 " model vdw 1.115 3.690 nonbonded pdb=" CB LEU E 27 " pdb=" CD2 HIS E 64 " model vdw 1.223 3.660 nonbonded pdb=" CG MET A 266 " pdb=" ND2 ASN A 272 " model vdw 1.260 3.520 nonbonded pdb=" CG1 VAL B 132 " pdb=" NE2 GLN B 141 " model vdw 1.266 3.540 nonbonded pdb=" O ILE B 51 " pdb=" CD1 LEU T 141 " model vdw 1.297 3.460 ... (remaining 380843 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.920 Check model and map are aligned: 0.700 Set scattering table: 0.400 Process input model: 146.520 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 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 : 0.009 0.109 48908 Z= 0.589 Angle : 1.662 60.289 66673 Z= 1.044 Chirality : 0.074 0.801 7416 Planarity : 0.012 0.247 8144 Dihedral : 17.154 174.056 19058 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 4.07 % Allowed : 8.69 % Favored : 87.24 % Rotamer: Outliers : 3.37 % Allowed : 5.86 % Favored : 90.77 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.12 (0.10), residues: 5525 helix: -0.35 (0.10), residues: 1965 sheet: -0.51 (0.18), residues: 733 loop : -2.51 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP U 298 HIS 0.029 0.003 HIS A 504 PHE 0.047 0.003 PHE R 216 TYR 0.053 0.005 TYR Q 105 ARG 0.082 0.006 ARG B 975 *********************** 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 2213 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 2047 time to evaluate : 5.215 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 GLN cc_start: 0.7987 (tp40) cc_final: 0.7768 (mt0) REVERT: A 27 SER cc_start: 0.7767 (t) cc_final: 0.7351 (m) REVERT: A 77 ASN cc_start: 0.5858 (p0) cc_final: 0.5442 (p0) REVERT: A 181 HIS cc_start: 0.2968 (OUTLIER) cc_final: 0.2168 (p90) REVERT: A 234 PHE cc_start: 0.5539 (t80) cc_final: 0.5078 (t80) REVERT: A 312 PHE cc_start: 0.7219 (t80) cc_final: 0.6954 (t80) REVERT: A 316 THR cc_start: 0.8646 (p) cc_final: 0.8007 (p) REVERT: A 510 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6636 (mt-10) REVERT: A 520 MET cc_start: 0.9081 (tpp) cc_final: 0.8269 (tpp) REVERT: A 542 LEU cc_start: 0.9042 (tp) cc_final: 0.8833 (tp) REVERT: A 765 ASN cc_start: 0.9058 (m-40) cc_final: 0.8522 (m110) REVERT: A 772 SER cc_start: 0.9199 (p) cc_final: 0.8771 (m) REVERT: A 777 SER cc_start: 0.8766 (p) cc_final: 0.8192 (m) REVERT: A 780 ASN cc_start: 0.8699 (m110) cc_final: 0.8286 (m-40) REVERT: A 828 LEU cc_start: 0.9270 (tp) cc_final: 0.9068 (tt) REVERT: A 894 ASP cc_start: 0.7584 (p0) cc_final: 0.7215 (t0) REVERT: A 1094 SER cc_start: 0.9438 (m) cc_final: 0.8734 (t) REVERT: A 1098 PRO cc_start: 0.5958 (Cg_endo) cc_final: 0.4970 (Cg_exo) REVERT: A 1130 ILE cc_start: 0.8468 (mm) cc_final: 0.8138 (mm) REVERT: A 1136 THR cc_start: 0.8104 (m) cc_final: 0.7902 (p) REVERT: A 1143 LEU cc_start: 0.7875 (mt) cc_final: 0.7610 (mt) REVERT: A 1166 LEU cc_start: 0.7023 (tp) cc_final: 0.6812 (tp) REVERT: A 1420 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.5916 (t0) REVERT: B 112 GLU cc_start: 0.7381 (tt0) cc_final: 0.7178 (tt0) REVERT: B 146 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6672 (tppp) REVERT: B 180 ASP cc_start: 0.7625 (t70) cc_final: 0.7006 (p0) REVERT: B 191 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8412 (mp0) REVERT: B 344 GLN cc_start: 0.5656 (pt0) cc_final: 0.5165 (tt0) REVERT: B 412 LEU cc_start: 0.8162 (tp) cc_final: 0.7940 (tt) REVERT: B 431 LEU cc_start: 0.8832 (tp) cc_final: 0.8571 (tp) REVERT: B 433 LEU cc_start: 0.8423 (mt) cc_final: 0.8106 (mt) REVERT: B 520 VAL cc_start: 0.9047 (m) cc_final: 0.8797 (t) REVERT: B 591 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6253 (ttt180) REVERT: B 666 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7520 (p0) REVERT: B 674 MET cc_start: 0.9105 (tpt) cc_final: 0.8903 (tpt) REVERT: B 690 CYS cc_start: 0.4979 (t) cc_final: 0.4166 (t) REVERT: B 785 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.8376 (t80) REVERT: B 847 LYS cc_start: 0.7073 (mttt) cc_final: 0.6802 (mtpp) REVERT: B 853 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 864 ASP cc_start: 0.7253 (m-30) cc_final: 0.6999 (m-30) REVERT: B 905 ASP cc_start: 0.7534 (t70) cc_final: 0.7299 (t0) REVERT: B 941 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8488 (tp40) REVERT: B 954 MET cc_start: 0.9159 (mmm) cc_final: 0.8528 (mmp) REVERT: B 976 MET cc_start: 0.8603 (mtm) cc_final: 0.7926 (mtm) REVERT: B 1022 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7741 (pt) REVERT: C 44 ILE cc_start: 0.9121 (tt) cc_final: 0.8844 (tt) REVERT: C 128 ILE cc_start: 0.8656 (tp) cc_final: 0.8181 (mm) REVERT: C 208 TYR cc_start: 0.7632 (m-80) cc_final: 0.6796 (m-80) REVERT: C 255 LYS cc_start: 0.7467 (tttp) cc_final: 0.7219 (tttm) REVERT: D 60 VAL cc_start: 0.5644 (t) cc_final: 0.5282 (t) REVERT: E 54 ARG cc_start: 0.1928 (OUTLIER) cc_final: 0.0737 (mtm180) REVERT: F 75 MET cc_start: 0.7680 (mmt) cc_final: 0.7330 (mmt) REVERT: F 91 LEU cc_start: 0.8188 (tp) cc_final: 0.7800 (tp) REVERT: F 97 LEU cc_start: 0.8566 (tp) cc_final: 0.8101 (tp) REVERT: H 1 MET cc_start: 0.2819 (ttt) cc_final: 0.2390 (ttp) REVERT: H 16 ASP cc_start: 0.4740 (t0) cc_final: 0.4451 (t0) REVERT: H 44 ASN cc_start: 0.8610 (t0) cc_final: 0.8291 (t0) REVERT: H 145 MET cc_start: 0.6220 (mtp) cc_final: 0.5721 (mtm) REVERT: I 1 MET cc_start: 0.1884 (mtt) cc_final: 0.1051 (mtt) REVERT: I 66 THR cc_start: 0.6230 (OUTLIER) cc_final: 0.5642 (p) REVERT: K 45 ILE cc_start: 0.8490 (tp) cc_final: 0.8065 (tp) REVERT: K 91 ILE cc_start: 0.7401 (mt) cc_final: 0.7175 (mt) REVERT: K 101 LEU cc_start: 0.8298 (tp) cc_final: 0.7949 (tp) REVERT: M 26 ASP cc_start: 0.5617 (t0) cc_final: 0.5178 (t0) REVERT: M 33 ILE cc_start: 0.7917 (mt) cc_final: 0.7582 (mt) REVERT: M 84 ILE cc_start: 0.7500 (pt) cc_final: 0.7020 (pt) REVERT: M 165 TYR cc_start: 0.8038 (t80) cc_final: 0.7657 (t80) REVERT: P 180 LEU cc_start: 0.5452 (mp) cc_final: 0.5147 (mp) REVERT: P 274 VAL cc_start: 0.6262 (p) cc_final: 0.6035 (p) REVERT: P 291 LEU cc_start: 0.7881 (tt) cc_final: 0.7565 (tt) REVERT: T 147 LYS cc_start: 0.3378 (OUTLIER) cc_final: 0.3099 (pttp) REVERT: T 209 PRO cc_start: 0.5490 (Cg_exo) cc_final: 0.5156 (Cg_endo) REVERT: U 252 LYS cc_start: -0.0630 (OUTLIER) cc_final: -0.2928 (mmmt) REVERT: U 285 MET cc_start: 0.2675 (ttp) cc_final: 0.2324 (tpp) outliers start: 166 outliers final: 45 residues processed: 2162 average time/residue: 0.6454 time to fit residues: 2198.4924 Evaluate side-chains 1379 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1321 time to evaluate : 5.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1319 LYS Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 897 ARG Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain Q residue 128 LYS Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain T residue 147 LYS Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 252 LYS Chi-restraints excluded: chain U residue 257 GLN Chi-restraints excluded: chain U residue 301 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 475 optimal weight: 5.9990 chunk 426 optimal weight: 8.9990 chunk 236 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 287 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 441 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 chunk 328 optimal weight: 0.2980 chunk 511 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS A 122 ASN A 181 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 461 GLN A 465 HIS ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 735 GLN A 739 ASN A 791 GLN ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1310 HIS ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1422 GLN A1445 HIS B 141 GLN B 287 HIS ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 631 GLN ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 GLN B 948 GLN C 60 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 129 GLN E 19 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 116 GLN E 132 GLN E 148 HIS ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN I 46 GLN I 60 HIS ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN K 40 HIS K 49 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN M 315 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN S 172 ASN ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 HIS U 270 ASN ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 48908 Z= 0.311 Angle : 0.917 17.726 66673 Z= 0.476 Chirality : 0.050 0.415 7416 Planarity : 0.007 0.183 8144 Dihedral : 17.674 175.765 7841 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 1.48 % Allowed : 8.05 % Favored : 90.46 % Rotamer: Outliers : 4.62 % Allowed : 17.56 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.15 % 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: -1.07 (0.11), residues: 5525 helix: 0.61 (0.11), residues: 2003 sheet: -0.08 (0.18), residues: 755 loop : -1.97 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 679 HIS 0.027 0.002 HIS R 108 PHE 0.039 0.002 PHE T 188 TYR 0.043 0.002 TYR C 3 ARG 0.017 0.001 ARG O 51 *********************** 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 1715 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1487 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7567 (mmm) cc_final: 0.7289 (tpp) REVERT: A 102 LYS cc_start: 0.6378 (mmtp) cc_final: 0.6081 (tppp) REVERT: A 107 LEU cc_start: 0.7327 (tp) cc_final: 0.7120 (tp) REVERT: A 118 LEU cc_start: 0.5817 (mm) cc_final: 0.5442 (mt) REVERT: A 316 THR cc_start: 0.8259 (p) cc_final: 0.7382 (p) REVERT: A 496 PHE cc_start: 0.8452 (m-80) cc_final: 0.8231 (m-80) REVERT: A 514 GLU cc_start: 0.7554 (tt0) cc_final: 0.7238 (tt0) REVERT: A 542 LEU cc_start: 0.8855 (tp) cc_final: 0.8315 (tp) REVERT: A 766 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: A 769 MET cc_start: 0.8849 (mtm) cc_final: 0.8450 (mtm) REVERT: A 777 SER cc_start: 0.8636 (p) cc_final: 0.8292 (t) REVERT: A 811 ILE cc_start: 0.9028 (tp) cc_final: 0.8790 (tt) REVERT: A 823 VAL cc_start: 0.8768 (t) cc_final: 0.7598 (t) REVERT: A 1094 SER cc_start: 0.9295 (m) cc_final: 0.8803 (t) REVERT: A 1403 ASP cc_start: 0.6666 (m-30) cc_final: 0.6369 (m-30) REVERT: A 1420 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6077 (t0) REVERT: A 1433 GLU cc_start: 0.5324 (mt-10) cc_final: 0.5064 (mt-10) REVERT: B 373 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7595 (mt) REVERT: B 414 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6130 (mm-30) REVERT: B 486 ASN cc_start: 0.8226 (t0) cc_final: 0.7707 (t0) REVERT: B 591 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.5861 (ttt180) REVERT: B 597 ILE cc_start: 0.7556 (tp) cc_final: 0.7235 (tp) REVERT: B 677 MET cc_start: 0.8267 (tpp) cc_final: 0.7995 (tpp) REVERT: B 690 CYS cc_start: 0.5072 (t) cc_final: 0.4661 (t) REVERT: B 741 HIS cc_start: 0.6791 (p-80) cc_final: 0.6575 (p90) REVERT: B 782 ILE cc_start: 0.9289 (mp) cc_final: 0.8948 (mt) REVERT: B 785 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 847 LYS cc_start: 0.6893 (mttt) cc_final: 0.6573 (mtpp) REVERT: B 864 ASP cc_start: 0.7224 (m-30) cc_final: 0.6837 (m-30) REVERT: C 44 ILE cc_start: 0.8904 (tt) cc_final: 0.8685 (tt) REVERT: C 263 LEU cc_start: 0.5639 (tp) cc_final: 0.5433 (tp) REVERT: E 138 ASN cc_start: 0.5626 (t0) cc_final: 0.5335 (t0) REVERT: E 204 ILE cc_start: 0.8661 (mt) cc_final: 0.8460 (mm) REVERT: F 107 ARG cc_start: 0.8510 (ttm170) cc_final: 0.8214 (ttm170) REVERT: G 14 HIS cc_start: 0.7872 (t-90) cc_final: 0.7459 (t-90) REVERT: G 72 TYR cc_start: 0.5413 (p90) cc_final: 0.5209 (p90) REVERT: H 1 MET cc_start: 0.2977 (ttt) cc_final: -0.1168 (mmp) REVERT: H 16 ASP cc_start: 0.4411 (t0) cc_final: 0.4190 (t0) REVERT: I 1 MET cc_start: 0.1695 (mtt) cc_final: 0.0745 (mtt) REVERT: I 54 TYR cc_start: 0.6883 (t80) cc_final: 0.6462 (t80) REVERT: K 102 GLU cc_start: 0.5285 (tm-30) cc_final: 0.4990 (tm-30) REVERT: L 44 MET cc_start: 0.7959 (mmm) cc_final: 0.7605 (mmm) REVERT: M 229 GLN cc_start: 0.7840 (tt0) cc_final: 0.7151 (tp40) REVERT: Q 25 PHE cc_start: 0.3384 (OUTLIER) cc_final: 0.3163 (m-80) REVERT: Q 110 MET cc_start: 0.5703 (mmp) cc_final: 0.5281 (mmp) REVERT: U 247 GLU cc_start: 0.6094 (tp30) cc_final: 0.5644 (mm-30) outliers start: 228 outliers final: 124 residues processed: 1604 average time/residue: 0.6411 time to fit residues: 1641.0458 Evaluate side-chains 1327 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1197 time to evaluate : 5.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 262 PRO Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1407 CYS Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 PRO Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 109 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 79 ASP Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 226 LYS Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 334 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 208 ARG Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 25 PHE Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 130 CYS Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 172 ASN Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 44 ARG Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain U residue 140 VAL Chi-restraints excluded: chain U residue 226 GLU Chi-restraints excluded: chain U residue 257 GLN Chi-restraints excluded: chain U residue 287 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 284 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 425 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 512 optimal weight: 7.9990 chunk 553 optimal weight: 6.9990 chunk 456 optimal weight: 0.9980 chunk 507 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 410 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 62 GLN ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 HIS ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 HIS ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 HIS ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 HIS ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN C 260 GLN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 ASN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 ASN ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 172 ASN ** S 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 48908 Z= 0.364 Angle : 0.876 14.859 66673 Z= 0.454 Chirality : 0.049 0.350 7416 Planarity : 0.007 0.175 8144 Dihedral : 17.308 176.390 7754 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 1.18 % Allowed : 8.62 % Favored : 90.21 % Rotamer: Outliers : 6.00 % Allowed : 19.83 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % 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: -0.99 (0.11), residues: 5525 helix: 0.54 (0.11), residues: 2012 sheet: -0.20 (0.18), residues: 775 loop : -1.76 (0.12), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 679 HIS 0.009 0.001 HIS B 577 PHE 0.028 0.002 PHE B 544 TYR 0.039 0.003 TYR R 84 ARG 0.010 0.001 ARG Q 16 *********************** 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 1553 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1257 time to evaluate : 4.504 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: A 15 LEU cc_start: 0.6001 (mt) cc_final: 0.5723 (mt) REVERT: A 34 MET cc_start: 0.7529 (mmm) cc_final: 0.7323 (tpp) REVERT: A 316 THR cc_start: 0.8314 (p) cc_final: 0.7871 (p) REVERT: A 338 SER cc_start: 0.8393 (p) cc_final: 0.7538 (t) REVERT: A 766 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: A 769 MET cc_start: 0.8963 (mtm) cc_final: 0.8554 (mtm) REVERT: A 777 SER cc_start: 0.8834 (p) cc_final: 0.8131 (t) REVERT: A 803 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7596 (mtpp) REVERT: A 811 ILE cc_start: 0.9128 (tp) cc_final: 0.8908 (tt) REVERT: A 988 TRP cc_start: 0.7603 (OUTLIER) cc_final: 0.7262 (t60) REVERT: A 1094 SER cc_start: 0.9291 (m) cc_final: 0.8866 (t) REVERT: A 1130 ILE cc_start: 0.8328 (mm) cc_final: 0.7933 (mm) REVERT: A 1403 ASP cc_start: 0.6947 (m-30) cc_final: 0.6587 (m-30) REVERT: A 1420 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.6905 (t0) REVERT: B 336 ILE cc_start: 0.6568 (mm) cc_final: 0.6359 (mm) REVERT: B 486 ASN cc_start: 0.8345 (t0) cc_final: 0.7818 (t0) REVERT: B 785 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7480 (t80) REVERT: B 846 ASP cc_start: 0.6485 (p0) cc_final: 0.6251 (p0) REVERT: B 951 GLN cc_start: 0.7559 (tt0) cc_final: 0.7268 (tt0) REVERT: B 976 MET cc_start: 0.8219 (mtm) cc_final: 0.7783 (mtp) REVERT: F 107 ARG cc_start: 0.8543 (ttm170) cc_final: 0.8258 (ttm170) REVERT: H 1 MET cc_start: 0.2819 (ttt) cc_final: -0.0675 (mmp) REVERT: H 67 ASP cc_start: 0.5480 (m-30) cc_final: 0.4962 (m-30) REVERT: I 1 MET cc_start: 0.1645 (mtt) cc_final: 0.1065 (mtt) REVERT: I 54 TYR cc_start: 0.6947 (t80) cc_final: 0.6643 (t80) REVERT: J 21 TYR cc_start: 0.8507 (t80) cc_final: 0.8278 (t80) REVERT: J 30 THR cc_start: 0.4027 (OUTLIER) cc_final: 0.3799 (p) REVERT: L 15 MET cc_start: 0.7310 (mpp) cc_final: 0.6726 (mpp) REVERT: M 179 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5603 (mt-10) REVERT: M 229 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: N 26 ARG cc_start: 0.4453 (tpm170) cc_final: 0.4127 (tpm170) REVERT: S 53 ASN cc_start: 0.3052 (p0) cc_final: 0.2828 (p0) REVERT: S 135 PHE cc_start: 0.2635 (OUTLIER) cc_final: 0.2038 (m-80) REVERT: U 205 ASN cc_start: 0.5306 (OUTLIER) cc_final: 0.4982 (p0) outliers start: 296 outliers final: 191 residues processed: 1407 average time/residue: 0.5930 time to fit residues: 1362.9992 Evaluate side-chains 1302 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1103 time to evaluate : 5.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 870 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 988 TRP Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1342 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1407 CYS Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 881 GLU Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 PRO Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 105 GLU Chi-restraints excluded: chain I residue 109 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 19 CYS Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 209 ILE Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 226 LYS Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 334 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 281 SER Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 76 MET Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain S residue 10 ASN Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 130 CYS Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 44 ARG Chi-restraints excluded: chain T residue 81 HIS Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 179 ASP Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain U residue 200 ASP Chi-restraints excluded: chain U residue 205 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 506 optimal weight: 8.9990 chunk 385 optimal weight: 0.3980 chunk 265 optimal weight: 0.8980 chunk 56 optimal weight: 0.0670 chunk 244 optimal weight: 1.9990 chunk 343 optimal weight: 8.9990 chunk 514 optimal weight: 10.0000 chunk 544 optimal weight: 9.9990 chunk 268 optimal weight: 0.5980 chunk 487 optimal weight: 9.9990 chunk 146 optimal weight: 0.0770 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 GLN A 472 HIS ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 HIS ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN D 46 GLN D 47 GLN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 107 GLN ** G 53 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 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 ASN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 167 ASN P 242 GLN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 ASN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 173 HIS T 91 GLN T 152 ASN ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 48908 Z= 0.234 Angle : 0.818 21.363 66673 Z= 0.419 Chirality : 0.047 0.379 7416 Planarity : 0.006 0.175 8144 Dihedral : 17.167 177.477 7745 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.86 % Favored : 91.19 % Rotamer: Outliers : 4.79 % Allowed : 22.59 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % 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: -0.91 (0.11), residues: 5525 helix: 0.54 (0.11), residues: 1994 sheet: -0.18 (0.17), residues: 811 loop : -1.64 (0.12), residues: 2720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP T 31 HIS 0.008 0.001 HIS Q 109 PHE 0.031 0.002 PHE M 306 TYR 0.045 0.002 TYR Q 20 ARG 0.012 0.001 ARG P 196 *********************** 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 1485 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1249 time to evaluate : 5.558 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: A 216 LEU cc_start: 0.7326 (mt) cc_final: 0.7071 (mt) REVERT: A 314 VAL cc_start: 0.8669 (m) cc_final: 0.8449 (t) REVERT: A 316 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 496 PHE cc_start: 0.8411 (m-80) cc_final: 0.8108 (m-80) REVERT: A 601 ASN cc_start: 0.7676 (m-40) cc_final: 0.6731 (m110) REVERT: A 766 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8395 (m-80) REVERT: A 777 SER cc_start: 0.8625 (p) cc_final: 0.8032 (t) REVERT: A 779 ILE cc_start: 0.8795 (mm) cc_final: 0.8503 (mt) REVERT: A 869 GLU cc_start: 0.6615 (pt0) cc_final: 0.6332 (pt0) REVERT: A 1094 SER cc_start: 0.9220 (m) cc_final: 0.8695 (t) REVERT: A 1130 ILE cc_start: 0.8368 (mm) cc_final: 0.8131 (mm) REVERT: A 1403 ASP cc_start: 0.6403 (m-30) cc_final: 0.5851 (m-30) REVERT: B 109 MET cc_start: 0.7239 (mmp) cc_final: 0.6851 (mmp) REVERT: B 217 TYR cc_start: 0.7242 (m-80) cc_final: 0.6826 (m-10) REVERT: B 336 ILE cc_start: 0.6630 (mm) cc_final: 0.6394 (mm) REVERT: B 373 LEU cc_start: 0.8054 (tt) cc_final: 0.7694 (mt) REVERT: B 414 GLU cc_start: 0.6508 (mm-30) cc_final: 0.6095 (mm-30) REVERT: B 486 ASN cc_start: 0.8256 (t0) cc_final: 0.7724 (t0) REVERT: B 782 ILE cc_start: 0.9145 (mp) cc_final: 0.8927 (mt) REVERT: B 785 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 846 ASP cc_start: 0.6474 (p0) cc_final: 0.6174 (p0) REVERT: B 864 ASP cc_start: 0.7502 (m-30) cc_final: 0.6227 (m-30) REVERT: B 976 MET cc_start: 0.8321 (mtm) cc_final: 0.8001 (mtp) REVERT: C 51 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7885 (tm-30) REVERT: F 107 ARG cc_start: 0.8673 (ttm170) cc_final: 0.8317 (ttm170) REVERT: H 1 MET cc_start: 0.2531 (ttt) cc_final: -0.0885 (mmp) REVERT: H 67 ASP cc_start: 0.5313 (m-30) cc_final: 0.4840 (m-30) REVERT: I 1 MET cc_start: 0.1722 (mtt) cc_final: 0.1056 (mtt) REVERT: J 21 TYR cc_start: 0.8310 (t80) cc_final: 0.7667 (t80) REVERT: M 229 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7440 (tp40) REVERT: P 207 PRO cc_start: 0.5705 (OUTLIER) cc_final: 0.5361 (Cg_endo) REVERT: P 313 THR cc_start: 0.5721 (t) cc_final: 0.5459 (t) REVERT: R 228 MET cc_start: 0.3038 (tpp) cc_final: 0.2505 (tpp) REVERT: S 135 PHE cc_start: 0.2335 (OUTLIER) cc_final: 0.1547 (m-80) outliers start: 236 outliers final: 146 residues processed: 1370 average time/residue: 0.5797 time to fit residues: 1300.2788 Evaluate side-chains 1269 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1117 time to evaluate : 5.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 209 ILE Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 309 VAL Chi-restraints excluded: chain N residue 334 VAL Chi-restraints excluded: chain N residue 352 HIS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 212 LEU Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 242 GLN Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain P residue 326 GLU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain R residue 230 GLU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 135 PHE Chi-restraints excluded: chain S residue 146 PHE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 44 ARG Chi-restraints excluded: chain T residue 81 HIS Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain U residue 200 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 453 optimal weight: 6.9990 chunk 308 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 224 optimal weight: 0.1980 chunk 464 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 488 optimal weight: 20.0000 chunk 137 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN F 49 GLN I 21 ASN ** I 45 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** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN P 229 GLN ** P 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 ASN ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 48908 Z= 0.311 Angle : 0.823 18.077 66673 Z= 0.423 Chirality : 0.047 0.299 7416 Planarity : 0.006 0.166 8144 Dihedral : 17.048 178.134 7741 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.54 % Favored : 90.59 % Rotamer: Outliers : 5.47 % Allowed : 23.50 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -0.91 (0.11), residues: 5525 helix: 0.54 (0.11), residues: 2001 sheet: -0.11 (0.18), residues: 794 loop : -1.66 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP T 31 HIS 0.016 0.001 HIS Q 109 PHE 0.032 0.002 PHE B 422 TYR 0.040 0.002 TYR A1197 ARG 0.009 0.001 ARG C 154 *********************** 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 1424 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1154 time to evaluate : 5.319 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: A 267 GLN cc_start: 0.5689 (tm-30) cc_final: 0.5440 (pp30) REVERT: A 314 VAL cc_start: 0.8737 (m) cc_final: 0.8501 (t) REVERT: A 500 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 565 MET cc_start: 0.8382 (tpt) cc_final: 0.8154 (tpp) REVERT: A 601 ASN cc_start: 0.7652 (m-40) cc_final: 0.6679 (m110) REVERT: A 766 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: A 777 SER cc_start: 0.8740 (p) cc_final: 0.8154 (t) REVERT: A 779 ILE cc_start: 0.8920 (mm) cc_final: 0.8587 (mt) REVERT: A 811 ILE cc_start: 0.8973 (tp) cc_final: 0.8756 (tt) REVERT: A 869 GLU cc_start: 0.6790 (pt0) cc_final: 0.6376 (pt0) REVERT: A 1094 SER cc_start: 0.9198 (m) cc_final: 0.8730 (t) REVERT: A 1130 ILE cc_start: 0.8445 (mm) cc_final: 0.8191 (mm) REVERT: A 1403 ASP cc_start: 0.6418 (m-30) cc_final: 0.6026 (m-30) REVERT: B 156 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 382 LEU cc_start: 0.7515 (mp) cc_final: 0.7182 (mp) REVERT: B 414 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6218 (mm-30) REVERT: B 486 ASN cc_start: 0.8257 (t0) cc_final: 0.7681 (t0) REVERT: B 497 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6562 (mmtt) REVERT: B 661 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8575 (t) REVERT: B 677 MET cc_start: 0.8263 (tpp) cc_final: 0.7914 (tpp) REVERT: B 782 ILE cc_start: 0.9208 (mp) cc_final: 0.8992 (mt) REVERT: B 785 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.7548 (t80) REVERT: B 846 ASP cc_start: 0.6404 (p0) cc_final: 0.6186 (p0) REVERT: E 84 ILE cc_start: 0.4304 (OUTLIER) cc_final: 0.3856 (mp) REVERT: F 107 ARG cc_start: 0.8761 (ttm170) cc_final: 0.8379 (ttm170) REVERT: H 1 MET cc_start: 0.2402 (ttt) cc_final: -0.1013 (mmp) REVERT: H 67 ASP cc_start: 0.5448 (m-30) cc_final: 0.5012 (m-30) REVERT: I 1 MET cc_start: 0.1883 (mtt) cc_final: 0.1122 (mtt) REVERT: M 229 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7520 (tp40) REVERT: P 207 PRO cc_start: 0.5727 (OUTLIER) cc_final: 0.5344 (Cg_endo) outliers start: 270 outliers final: 193 residues processed: 1290 average time/residue: 0.5867 time to fit residues: 1253.1541 Evaluate side-chains 1282 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1081 time to evaluate : 5.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 854 ILE Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 209 ILE Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 352 HIS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain S residue 146 PHE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 29 GLN Chi-restraints excluded: chain T residue 44 ARG Chi-restraints excluded: chain T residue 81 HIS Chi-restraints excluded: chain T residue 143 GLN Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain U residue 200 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 183 optimal weight: 0.6980 chunk 490 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 319 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 544 optimal weight: 4.9990 chunk 452 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 285 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 319 ASN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 46 GLN ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 171 GLN U 197 ASN U 270 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 48908 Z= 0.260 Angle : 0.806 16.914 66673 Z= 0.414 Chirality : 0.047 0.499 7416 Planarity : 0.006 0.161 8144 Dihedral : 16.972 178.491 7738 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.78 % Allowed : 8.34 % Favored : 90.88 % Rotamer: Outliers : 5.33 % Allowed : 24.25 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -0.93 (0.11), residues: 5525 helix: 0.53 (0.11), residues: 2001 sheet: -0.26 (0.17), residues: 835 loop : -1.64 (0.12), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP T 31 HIS 0.012 0.001 HIS B 577 PHE 0.041 0.002 PHE T 188 TYR 0.035 0.002 TYR A1197 ARG 0.009 0.001 ARG A 186 *********************** 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 1399 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1136 time to evaluate : 5.262 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: A 314 VAL cc_start: 0.8695 (m) cc_final: 0.8353 (t) REVERT: A 523 ARG cc_start: 0.8426 (tpp-160) cc_final: 0.7889 (ttm110) REVERT: A 777 SER cc_start: 0.8759 (p) cc_final: 0.8150 (t) REVERT: A 779 ILE cc_start: 0.8894 (mm) cc_final: 0.8541 (mt) REVERT: A 869 GLU cc_start: 0.6672 (pt0) cc_final: 0.6288 (pt0) REVERT: A 1094 SER cc_start: 0.9171 (m) cc_final: 0.8707 (t) REVERT: A 1130 ILE cc_start: 0.8508 (mm) cc_final: 0.8237 (mm) REVERT: A 1262 MET cc_start: 0.4470 (mmm) cc_final: 0.4003 (mmm) REVERT: A 1403 ASP cc_start: 0.6379 (m-30) cc_final: 0.5991 (m-30) REVERT: A 1434 GLU cc_start: 0.6854 (mp0) cc_final: 0.6644 (mp0) REVERT: B 109 MET cc_start: 0.7027 (mmp) cc_final: 0.6732 (mmp) REVERT: B 414 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6053 (mm-30) REVERT: B 486 ASN cc_start: 0.8283 (t0) cc_final: 0.7676 (t0) REVERT: B 550 MET cc_start: 0.8026 (tmm) cc_final: 0.7804 (tmm) REVERT: B 675 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8654 (tp) REVERT: B 782 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8886 (mt) REVERT: B 785 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.7638 (t80) REVERT: B 846 ASP cc_start: 0.6476 (p0) cc_final: 0.6111 (p0) REVERT: B 1072 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7979 (mmt90) REVERT: C 14 LEU cc_start: 0.7845 (tt) cc_final: 0.7544 (mp) REVERT: F 107 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8360 (ttm170) REVERT: I 1 MET cc_start: 0.1723 (mtt) cc_final: 0.0706 (mtt) REVERT: K 38 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6573 (mm-30) REVERT: M 229 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: M 273 GLU cc_start: 0.6157 (tp30) cc_final: 0.5831 (tp30) REVERT: P 178 LEU cc_start: 0.5478 (mt) cc_final: 0.5141 (tt) REVERT: P 207 PRO cc_start: 0.5557 (OUTLIER) cc_final: 0.5142 (Cg_endo) REVERT: T 143 GLN cc_start: 0.2726 (OUTLIER) cc_final: 0.1803 (pm20) outliers start: 263 outliers final: 194 residues processed: 1265 average time/residue: 0.5899 time to fit residues: 1230.4841 Evaluate side-chains 1256 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1056 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1342 SER Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 85 PRO Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 209 ILE Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 243 ASP Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 334 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain N residue 365 TYR Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 263 ASP Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain R residue 220 TRP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain S residue 146 PHE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 166 ARG Chi-restraints excluded: chain T residue 31 TRP Chi-restraints excluded: chain T residue 44 ARG Chi-restraints excluded: chain T residue 81 HIS Chi-restraints excluded: chain T residue 143 GLN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 197 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 525 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 310 optimal weight: 8.9990 chunk 397 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 chunk 458 optimal weight: 0.9990 chunk 304 optimal weight: 0.0970 chunk 542 optimal weight: 4.9990 chunk 339 optimal weight: 4.9990 chunk 330 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 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 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 319 ASN B 456 GLN B1030 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 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** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 48908 Z= 0.245 Angle : 0.806 18.199 66673 Z= 0.414 Chirality : 0.047 0.482 7416 Planarity : 0.006 0.164 8144 Dihedral : 16.907 178.890 7735 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.34 % Favored : 90.91 % Rotamer: Outliers : 5.13 % Allowed : 24.88 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -0.88 (0.11), residues: 5525 helix: 0.53 (0.11), residues: 1993 sheet: -0.17 (0.17), residues: 839 loop : -1.61 (0.12), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 988 HIS 0.012 0.001 HIS B 577 PHE 0.036 0.002 PHE S 110 TYR 0.029 0.002 TYR Q 188 ARG 0.011 0.001 ARG B 405 *********************** 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 1378 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1125 time to evaluate : 5.305 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 272 ASN cc_start: 0.3923 (OUTLIER) cc_final: 0.3184 (p0) REVERT: A 314 VAL cc_start: 0.8644 (m) cc_final: 0.8318 (t) REVERT: A 523 ARG cc_start: 0.8229 (tpp-160) cc_final: 0.7727 (ttm110) REVERT: A 777 SER cc_start: 0.8815 (p) cc_final: 0.8080 (t) REVERT: A 779 ILE cc_start: 0.8850 (mm) cc_final: 0.8510 (mt) REVERT: A 869 GLU cc_start: 0.6726 (pt0) cc_final: 0.6426 (pt0) REVERT: A 1094 SER cc_start: 0.9148 (m) cc_final: 0.8717 (t) REVERT: A 1130 ILE cc_start: 0.8547 (mm) cc_final: 0.8266 (mm) REVERT: A 1403 ASP cc_start: 0.6384 (m-30) cc_final: 0.5955 (m-30) REVERT: A 1420 ASN cc_start: 0.6947 (t0) cc_final: 0.6640 (t0) REVERT: A 1434 GLU cc_start: 0.6706 (mp0) cc_final: 0.6490 (mp0) REVERT: B 109 MET cc_start: 0.7078 (mmp) cc_final: 0.6775 (mmp) REVERT: B 336 ILE cc_start: 0.6648 (mm) cc_final: 0.6321 (mm) REVERT: B 414 GLU cc_start: 0.6448 (mm-30) cc_final: 0.6085 (mm-30) REVERT: B 486 ASN cc_start: 0.8281 (t0) cc_final: 0.7655 (t0) REVERT: B 550 MET cc_start: 0.8024 (tmm) cc_final: 0.7756 (tmm) REVERT: B 661 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8352 (t) REVERT: B 675 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8648 (tp) REVERT: B 782 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8854 (mt) REVERT: B 785 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7646 (t80) REVERT: B 846 ASP cc_start: 0.6497 (p0) cc_final: 0.6178 (p0) REVERT: C 14 LEU cc_start: 0.7902 (tt) cc_final: 0.7575 (mp) REVERT: F 91 LEU cc_start: 0.8130 (mt) cc_final: 0.7339 (mm) REVERT: F 107 ARG cc_start: 0.8778 (ttm170) cc_final: 0.8378 (ttm170) REVERT: G 4 HIS cc_start: 0.3456 (OUTLIER) cc_final: 0.3189 (t70) REVERT: H 1 MET cc_start: 0.2679 (ttt) cc_final: 0.0348 (mmm) REVERT: I 1 MET cc_start: 0.1877 (mtt) cc_final: 0.0686 (mtt) REVERT: I 100 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.4911 (m90) REVERT: M 229 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7507 (tp40) REVERT: P 207 PRO cc_start: 0.5496 (OUTLIER) cc_final: 0.5097 (Cg_endo) REVERT: P 270 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5814 (mp) REVERT: S 177 MET cc_start: 0.3000 (mtp) cc_final: 0.2770 (mtm) outliers start: 253 outliers final: 194 residues processed: 1256 average time/residue: 0.5895 time to fit residues: 1225.4376 Evaluate side-chains 1259 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1055 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1167 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 21 ASN Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 76 SER Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 243 ASP Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 40 PHE Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 263 ASP Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 194 ARG Chi-restraints excluded: chain R residue 220 TRP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain S residue 146 PHE Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 166 ARG Chi-restraints excluded: chain T residue 29 GLN Chi-restraints excluded: chain T residue 31 TRP Chi-restraints excluded: chain T residue 44 ARG Chi-restraints excluded: chain T residue 81 HIS Chi-restraints excluded: chain T residue 143 GLN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 183 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 200 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 335 optimal weight: 0.0670 chunk 216 optimal weight: 0.5980 chunk 324 optimal weight: 0.0040 chunk 163 optimal weight: 0.9990 chunk 106 optimal weight: 0.0030 chunk 105 optimal weight: 0.9990 chunk 344 optimal weight: 4.9990 chunk 369 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 426 optimal weight: 7.9990 overall best weight: 0.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 529 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 ASN ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 654 GLN B1030 ASN B1071 ASN C 66 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 GLN ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN U 270 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 48908 Z= 0.219 Angle : 0.835 28.638 66673 Z= 0.421 Chirality : 0.047 0.449 7416 Planarity : 0.006 0.207 8144 Dihedral : 16.853 179.217 7731 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.09 % Favored : 91.22 % Rotamer: Outliers : 3.83 % Allowed : 26.91 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 2.02 % 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: -0.84 (0.11), residues: 5525 helix: 0.53 (0.11), residues: 1980 sheet: -0.19 (0.17), residues: 837 loop : -1.52 (0.12), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 988 HIS 0.010 0.001 HIS B 577 PHE 0.083 0.002 PHE S 110 TYR 0.037 0.002 TYR A1197 ARG 0.013 0.001 ARG A 407 *********************** 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 1363 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1174 time to evaluate : 5.427 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: A 77 ASN cc_start: 0.6044 (p0) cc_final: 0.5816 (p0) REVERT: A 314 VAL cc_start: 0.8654 (m) cc_final: 0.8278 (t) REVERT: A 523 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7694 (ttm110) REVERT: A 777 SER cc_start: 0.8795 (p) cc_final: 0.7911 (m) REVERT: A 779 ILE cc_start: 0.8786 (mm) cc_final: 0.8450 (mt) REVERT: A 869 GLU cc_start: 0.6576 (pt0) cc_final: 0.6315 (pt0) REVERT: A 1094 SER cc_start: 0.9131 (m) cc_final: 0.8827 (t) REVERT: A 1130 ILE cc_start: 0.8541 (mm) cc_final: 0.8264 (mm) REVERT: A 1403 ASP cc_start: 0.6158 (m-30) cc_final: 0.5641 (m-30) REVERT: B 414 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5881 (mm-30) REVERT: B 550 MET cc_start: 0.7963 (tmm) cc_final: 0.7758 (tmm) REVERT: B 782 ILE cc_start: 0.9105 (mp) cc_final: 0.8815 (mt) REVERT: B 785 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7607 (t80) REVERT: B 846 ASP cc_start: 0.6580 (p0) cc_final: 0.6158 (p0) REVERT: C 14 LEU cc_start: 0.7940 (tt) cc_final: 0.7613 (mp) REVERT: C 94 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.6987 (p) REVERT: E 110 MET cc_start: 0.5941 (tpp) cc_final: 0.5411 (tpt) REVERT: F 90 LEU cc_start: 0.8927 (tp) cc_final: 0.8581 (tp) REVERT: F 102 ILE cc_start: 0.8084 (mp) cc_final: 0.7736 (mt) REVERT: F 107 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8399 (ttm170) REVERT: H 1 MET cc_start: 0.2580 (ttt) cc_final: -0.0886 (mmp) REVERT: I 1 MET cc_start: 0.1800 (mtt) cc_final: 0.0578 (mtt) REVERT: I 100 HIS cc_start: 0.5442 (OUTLIER) cc_final: 0.4873 (m90) REVERT: M 229 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7626 (tp40) REVERT: P 207 PRO cc_start: 0.5434 (OUTLIER) cc_final: 0.5140 (Cg_endo) REVERT: P 262 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7125 (m) REVERT: P 270 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5721 (mp) REVERT: P 313 THR cc_start: 0.4885 (t) cc_final: 0.4648 (t) REVERT: R 228 MET cc_start: 0.3153 (tpp) cc_final: 0.2809 (tpp) REVERT: S 151 ARG cc_start: 0.5188 (mmp-170) cc_final: 0.4919 (mmp-170) REVERT: T 145 LEU cc_start: 0.6349 (tp) cc_final: 0.5949 (tp) REVERT: U 285 MET cc_start: 0.1321 (tpt) cc_final: 0.0974 (tpt) outliers start: 189 outliers final: 144 residues processed: 1265 average time/residue: 0.5939 time to fit residues: 1241.2241 Evaluate side-chains 1244 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1093 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 790 GLN Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 32 ASN Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 243 ASP Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 191 GLU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 270 LEU Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 180 PHE Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 220 TRP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain S residue 144 TYR Chi-restraints excluded: chain S residue 146 PHE Chi-restraints excluded: chain S residue 166 ARG Chi-restraints excluded: chain T residue 29 GLN Chi-restraints excluded: chain T residue 31 TRP Chi-restraints excluded: chain T residue 44 ARG Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 143 GLN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 197 ASN Chi-restraints excluded: chain U residue 200 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 493 optimal weight: 20.0000 chunk 519 optimal weight: 8.9990 chunk 474 optimal weight: 10.0000 chunk 505 optimal weight: 0.9990 chunk 304 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 397 optimal weight: 3.9990 chunk 155 optimal weight: 0.0470 chunk 456 optimal weight: 4.9990 chunk 478 optimal weight: 9.9990 chunk 503 optimal weight: 8.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 609 HIS A 731 ASN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 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 111 ASN B1030 ASN C 66 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 116 GLN ** E 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 ASN O 16 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 229 GLN ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN U 270 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.6606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 48908 Z= 0.331 Angle : 0.864 22.170 66673 Z= 0.439 Chirality : 0.049 0.416 7416 Planarity : 0.006 0.184 8144 Dihedral : 16.867 179.303 7727 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.63 % Favored : 90.71 % Rotamer: Outliers : 4.30 % Allowed : 27.15 % Favored : 68.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.96 (0.11), residues: 5525 helix: 0.42 (0.11), residues: 2007 sheet: -0.34 (0.17), residues: 823 loop : -1.57 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP A 988 HIS 0.021 0.002 HIS A 278 PHE 0.146 0.003 PHE S 110 TYR 0.031 0.002 TYR C 3 ARG 0.014 0.001 ARG E 162 *********************** 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 1310 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1098 time to evaluate : 5.312 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 314 VAL cc_start: 0.8706 (m) cc_final: 0.8372 (t) REVERT: A 523 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7678 (ttm110) REVERT: A 565 MET cc_start: 0.8164 (tpt) cc_final: 0.7893 (tpp) REVERT: A 777 SER cc_start: 0.8821 (p) cc_final: 0.8084 (t) REVERT: A 779 ILE cc_start: 0.8832 (mm) cc_final: 0.8554 (mt) REVERT: A 869 GLU cc_start: 0.6648 (pt0) cc_final: 0.6301 (pt0) REVERT: A 1094 SER cc_start: 0.9282 (m) cc_final: 0.8799 (t) REVERT: A 1130 ILE cc_start: 0.8549 (mm) cc_final: 0.8297 (mm) REVERT: A 1403 ASP cc_start: 0.6305 (m-30) cc_final: 0.5869 (m-30) REVERT: B 414 GLU cc_start: 0.6480 (mm-30) cc_final: 0.6128 (mm-30) REVERT: B 491 ARG cc_start: -0.0055 (OUTLIER) cc_final: -0.1533 (tmt170) REVERT: B 550 MET cc_start: 0.8067 (tmm) cc_final: 0.7802 (tmm) REVERT: B 675 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8716 (tp) REVERT: B 782 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8912 (mt) REVERT: B 785 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.7744 (t80) REVERT: B 846 ASP cc_start: 0.6633 (p0) cc_final: 0.6221 (p0) REVERT: C 94 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7004 (p) REVERT: E 19 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.6267 (tp40) REVERT: E 194 ILE cc_start: 0.9307 (mp) cc_final: 0.9011 (mt) REVERT: F 98 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7489 (tppt) REVERT: F 107 ARG cc_start: 0.8723 (ttm170) cc_final: 0.8382 (ttm170) REVERT: H 1 MET cc_start: 0.2877 (ttt) cc_final: -0.0999 (mmp) REVERT: I 1 MET cc_start: 0.1830 (mtt) cc_final: 0.0510 (mtt) REVERT: I 100 HIS cc_start: 0.5462 (OUTLIER) cc_final: 0.4910 (m90) REVERT: K 97 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5800 (tp30) REVERT: M 229 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7594 (tp40) REVERT: P 207 PRO cc_start: 0.5498 (OUTLIER) cc_final: 0.5206 (Cg_endo) REVERT: R 228 MET cc_start: 0.3331 (tpp) cc_final: 0.3043 (tpp) REVERT: T 145 LEU cc_start: 0.6534 (tp) cc_final: 0.6163 (tp) outliers start: 212 outliers final: 161 residues processed: 1218 average time/residue: 0.5792 time to fit residues: 1164.1101 Evaluate side-chains 1228 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1058 time to evaluate : 5.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 36 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 243 ASP Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 350 LYS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 191 GLU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 263 ASP Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 180 PHE Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 220 TRP Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain S residue 144 TYR Chi-restraints excluded: chain S residue 146 PHE Chi-restraints excluded: chain S residue 166 ARG Chi-restraints excluded: chain T residue 29 GLN Chi-restraints excluded: chain T residue 31 TRP Chi-restraints excluded: chain T residue 81 HIS Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 143 GLN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 182 HIS Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 332 optimal weight: 2.9990 chunk 534 optimal weight: 10.0000 chunk 326 optimal weight: 0.6980 chunk 253 optimal weight: 1.9990 chunk 371 optimal weight: 0.7980 chunk 560 optimal weight: 8.9990 chunk 516 optimal weight: 0.0040 chunk 446 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 344 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B1030 ASN C 66 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 116 GLN E 168 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN U 270 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 48908 Z= 0.277 Angle : 0.872 18.887 66673 Z= 0.443 Chirality : 0.049 0.406 7416 Planarity : 0.006 0.133 8144 Dihedral : 16.884 179.339 7726 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.65 % Favored : 90.73 % Rotamer: Outliers : 3.87 % Allowed : 27.70 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.00 (0.11), residues: 5525 helix: 0.38 (0.11), residues: 2000 sheet: -0.37 (0.17), residues: 833 loop : -1.58 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 988 HIS 0.017 0.001 HIS A 278 PHE 0.149 0.003 PHE S 110 TYR 0.047 0.002 TYR Q 20 ARG 0.016 0.001 ARG E 162 ********************** 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 1297 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1106 time to evaluate : 5.287 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 314 VAL cc_start: 0.8699 (m) cc_final: 0.8318 (t) REVERT: A 523 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7712 (ttm110) REVERT: A 565 MET cc_start: 0.8080 (tpt) cc_final: 0.7837 (tpp) REVERT: A 777 SER cc_start: 0.8851 (p) cc_final: 0.8037 (t) REVERT: A 779 ILE cc_start: 0.8794 (mm) cc_final: 0.8519 (mt) REVERT: A 1094 SER cc_start: 0.9178 (m) cc_final: 0.8794 (t) REVERT: A 1130 ILE cc_start: 0.8522 (mm) cc_final: 0.8245 (mm) REVERT: A 1403 ASP cc_start: 0.6220 (m-30) cc_final: 0.5845 (m-30) REVERT: B 336 ILE cc_start: 0.6500 (mm) cc_final: 0.6202 (mm) REVERT: B 414 GLU cc_start: 0.6426 (mm-30) cc_final: 0.6056 (mm-30) REVERT: B 491 ARG cc_start: -0.0190 (OUTLIER) cc_final: -0.1602 (tmt170) REVERT: B 550 MET cc_start: 0.8042 (tmm) cc_final: 0.7718 (tmm) REVERT: B 675 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8679 (tp) REVERT: B 782 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8876 (mt) REVERT: B 785 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.7611 (t80) REVERT: B 790 GLN cc_start: 0.8301 (mt0) cc_final: 0.7691 (mm-40) REVERT: B 846 ASP cc_start: 0.6737 (p0) cc_final: 0.6354 (p0) REVERT: C 94 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6932 (p) REVERT: D 74 PHE cc_start: 0.4440 (m-80) cc_final: 0.4204 (m-10) REVERT: E 194 ILE cc_start: 0.9281 (mp) cc_final: 0.9001 (mt) REVERT: F 90 LEU cc_start: 0.8837 (tp) cc_final: 0.8589 (tp) REVERT: F 98 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7492 (tppt) REVERT: F 102 ILE cc_start: 0.8187 (mp) cc_final: 0.7861 (mt) REVERT: F 107 ARG cc_start: 0.8762 (ttm170) cc_final: 0.8378 (ttm170) REVERT: G 4 HIS cc_start: 0.3360 (OUTLIER) cc_final: 0.3136 (t70) REVERT: G 16 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7509 (ptp-110) REVERT: H 1 MET cc_start: 0.2859 (ttt) cc_final: -0.0997 (mmp) REVERT: I 1 MET cc_start: 0.1916 (mtt) cc_final: 0.0636 (mtt) REVERT: I 100 HIS cc_start: 0.5410 (OUTLIER) cc_final: 0.4861 (m90) REVERT: K 97 GLU cc_start: 0.6045 (mm-30) cc_final: 0.5837 (tp30) REVERT: L 44 MET cc_start: 0.8191 (mmm) cc_final: 0.7578 (mmm) REVERT: M 229 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7587 (tp40) REVERT: P 207 PRO cc_start: 0.5495 (OUTLIER) cc_final: 0.5196 (Cg_endo) REVERT: P 262 CYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7097 (m) REVERT: R 228 MET cc_start: 0.3344 (tpp) cc_final: 0.3010 (tpp) REVERT: S 178 GLN cc_start: 0.5020 (mm-40) cc_final: 0.4706 (mm-40) REVERT: T 143 GLN cc_start: 0.2808 (OUTLIER) cc_final: 0.0403 (pt0) REVERT: T 145 LEU cc_start: 0.6496 (tp) cc_final: 0.6009 (tp) REVERT: U 185 MET cc_start: 0.5638 (tpt) cc_final: 0.5340 (tpt) outliers start: 191 outliers final: 154 residues processed: 1215 average time/residue: 0.5824 time to fit residues: 1168.4789 Evaluate side-chains 1242 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1077 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 623 PRO Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 947 HIS Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1026 ASP Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1347 LEU Chi-restraints excluded: chain A residue 1422 GLN Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 711 ILE Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 801 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 895 PHE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 958 CYS Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 977 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 17 TYR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 141 LEU Chi-restraints excluded: chain M residue 144 GLN Chi-restraints excluded: chain M residue 149 LYS Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 229 GLN Chi-restraints excluded: chain M residue 260 MET Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 353 LEU Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 207 PRO Chi-restraints excluded: chain P residue 209 THR Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 244 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 262 CYS Chi-restraints excluded: chain P residue 263 ASP Chi-restraints excluded: chain P residue 268 ILE Chi-restraints excluded: chain P residue 307 SER Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 105 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 180 PHE Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 226 ASP Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain S residue 144 TYR Chi-restraints excluded: chain S residue 146 PHE Chi-restraints excluded: chain S residue 166 ARG Chi-restraints excluded: chain T residue 29 GLN Chi-restraints excluded: chain T residue 81 HIS Chi-restraints excluded: chain T residue 141 LEU Chi-restraints excluded: chain T residue 143 GLN Chi-restraints excluded: chain T residue 156 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 211 VAL Chi-restraints excluded: chain U residue 197 ASN Chi-restraints excluded: chain U residue 270 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 563 random chunks: chunk 354 optimal weight: 2.9990 chunk 475 optimal weight: 20.0000 chunk 136 optimal weight: 0.9980 chunk 411 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 447 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 459 optimal weight: 0.0370 chunk 56 optimal weight: 0.0370 chunk 82 optimal weight: 3.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1251 ASN ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B1030 ASN C 66 HIS ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN E 19 GLN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN U 270 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.168166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121572 restraints weight = 96463.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118014 restraints weight = 76388.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119457 restraints weight = 78922.125| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 48908 Z= 0.253 Angle : 0.871 19.321 66673 Z= 0.441 Chirality : 0.048 0.437 7416 Planarity : 0.006 0.133 8144 Dihedral : 16.872 179.467 7726 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.34 % Favored : 91.04 % Rotamer: Outliers : 3.51 % Allowed : 28.18 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.98 (0.11), residues: 5525 helix: 0.43 (0.11), residues: 1997 sheet: -0.38 (0.17), residues: 831 loop : -1.58 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP A 988 HIS 0.014 0.001 HIS A 278 PHE 0.086 0.002 PHE S 110 TYR 0.031 0.002 TYR R 84 ARG 0.015 0.001 ARG E 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18415.37 seconds wall clock time: 326 minutes 9.29 seconds (19569.29 seconds total)