Starting phenix.real_space_refine (version: dev) on Thu Dec 22 10:51:41 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/12_2022/5iyc_8137.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/12_2022/5iyc_8137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/12_2022/5iyc_8137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/12_2022/5iyc_8137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/12_2022/5iyc_8137.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5iyc_8137/12_2022/5iyc_8137.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 219": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 645": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B ARG 897": "NH1" <-> "NH2" Residue "B GLU 1105": "OE1" <-> "OE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "I ARG 33": "NH1" <-> "NH2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 28": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M ARG 105": "NH1" <-> "NH2" Residue "M ARG 112": "NH1" <-> "NH2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M ARG 248": "NH1" <-> "NH2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "N ASP 340": "OD1" <-> "OD2" Residue "N ARG 363": "NH1" <-> "NH2" Residue "O GLU 21": "OE1" <-> "OE2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P GLU 206": "OE1" <-> "OE2" Residue "P ARG 208": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 269": "NH1" <-> "NH2" Residue "P ARG 294": "NH1" <-> "NH2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P ARG 336": "NH1" <-> "NH2" Residue "Q ARG 174": "NH1" <-> "NH2" Residue "Q ARG 179": "NH1" <-> "NH2" Residue "Q ARG 192": "NH1" <-> "NH2" Residue "R GLU 169": "OE1" <-> "OE2" Residue "R ASP 213": "OD1" <-> "OD2" Residue "R GLU 230": "OE1" <-> "OE2" Residue "R GLU 234": "OE1" <-> "OE2" Residue "S GLU 136": "OE1" <-> "OE2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T GLU 133": "OE1" <-> "OE2" Residue "U ARG 192": "NH1" <-> "NH2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "U GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 47927 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1454, 11515 Classifications: {'peptide': 1454} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1384} Chain breaks: 1 Chain: "B" Number of atoms: 9317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9317 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 53, 'TRANS': 1111} Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2213 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "D" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1062 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1723 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 689 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1205 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "I" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1013 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 937 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2391 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 16, 'TRANS': 293} Chain: "N" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "P" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain: "Q" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1484 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1357 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain: "S" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "T" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Chain: "U" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1343 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "X" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1645 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "Y" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1624 Classifications: {'DNA': 80} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 79} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 52.496 116.861 106.459 1.00 0.00 S ATOM 494 SG CYS A 74 51.834 120.887 107.486 1.00 0.00 S ATOM 541 SG CYS A 81 53.736 118.771 104.063 1.00 0.00 S ATOM 776 SG CYS A 111 100.613 118.808 114.297 1.00 0.00 S ATOM 804 SG CYS A 114 100.325 120.420 118.319 1.00 0.00 S ATOM 1117 SG CYS A 154 103.357 120.580 115.564 1.00 0.00 S ATOM 1162 SG CYS A 184 102.525 116.811 117.366 1.00 0.00 S ATOM 20402 SG CYS B1119 63.038 131.166 113.345 1.00 0.00 S ATOM 20424 SG CYS B1122 66.171 128.694 112.348 1.00 0.00 S ATOM 20539 SG CYS B1137 62.043 127.322 113.528 1.00 0.00 S ATOM 20560 SG CYS B1140 65.317 128.308 115.652 1.00 0.00 S ATOM 21535 SG CYS C 88 10.588 127.248 52.370 1.00 0.00 S ATOM 21548 SG CYS C 90 11.666 123.927 54.909 1.00 0.00 S ATOM 21583 SG CYS C 94 9.643 123.490 51.663 1.00 0.00 S ATOM 21605 SG CYS C 97 13.399 124.088 51.386 1.00 0.00 S ATOM 29208 SG CYS I 17 130.635 89.377 62.996 1.00 0.00 S ATOM 29232 SG CYS I 20 127.730 88.786 65.147 1.00 0.00 S ATOM 29393 SG CYS I 39 128.703 91.811 66.272 1.00 0.00 S ATOM 29418 SG CYS I 42 131.132 88.917 66.797 1.00 0.00 S ATOM 29770 SG CYS I 86 114.022 106.936 24.394 1.00 0.00 S ATOM 29794 SG CYS I 89 112.841 104.933 21.484 1.00 0.00 S ATOM 29998 SG CYS I 114 111.111 104.955 24.914 1.00 0.00 S ATOM 30033 SG CYS I 119 115.057 103.571 24.121 1.00 0.00 S ATOM 30143 SG CYS J 7 40.276 122.721 34.835 1.00 0.00 S ATOM 30167 SG CYS J 10 38.429 125.267 33.207 1.00 0.00 S ATOM 30431 SG CYS J 44 42.174 125.023 32.224 1.00 0.00 S ATOM 30437 SG CYS J 45 39.294 123.124 30.629 1.00 0.00 S ATOM 31616 SG CYS L 19 36.136 86.898 60.207 1.00 0.00 S ATOM 31635 SG CYS L 22 33.508 85.778 57.877 1.00 0.00 S ATOM 31752 SG CYS L 36 33.088 84.428 61.180 1.00 0.00 S ATOM 31778 SG CYS L 39 36.763 83.294 58.618 1.00 0.00 S ATOM 32013 SG CYS M 15 29.338 123.746 97.070 1.00 0.00 S ATOM 32160 SG CYS M 34 29.436 121.542 93.642 1.00 0.00 S ATOM 32182 SG CYS M 37 28.238 125.387 93.598 1.00 0.00 S ATOM 38417 SG CYS Q 129 36.550 114.091 127.056 1.00 0.00 S ATOM 38437 SG CYS Q 132 39.763 113.670 124.846 1.00 0.00 S ATOM 38609 SG CYS Q 154 38.164 117.134 124.907 1.00 0.00 S ATOM 38633 SG CYS Q 157 36.423 114.241 123.143 1.00 0.00 S ATOM 44342 SG CYS U 263 87.514 156.413 48.454 1.00 0.00 S ATOM 44361 SG CYS U 266 91.492 157.050 48.400 1.00 0.00 S ATOM 44559 SG CYS U 291 89.751 153.469 48.929 1.00 0.00 S ATOM 44582 SG CYS U 294 89.670 156.177 51.799 1.00 0.00 S Time building chain proxies: 25.43, per 1000 atoms: 0.53 Number of scatterers: 47927 At special positions: 0 Unit cell: (180.78, 209.6, 170.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 11 29.99 S 270 16.00 P 158 15.00 Mg 2 11.99 O 9371 8.00 N 8418 7.00 C 29697 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.88 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb=" ZN Q 501 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 154 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 157 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 129 " pdb="ZN ZN Q 501 " - pdb=" SG CYS Q 132 " pdb=" ZN U 401 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 291 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 266 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 294 " pdb="ZN ZN U 401 " - pdb=" SG CYS U 263 " Number of angles added : 60 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10528 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 56 sheets defined 41.3% alpha, 18.9% beta 49 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 14.51 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.537A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.568A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.672A pdb=" N CYS A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 300 through 319 Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.318A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.501A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.630A pdb=" N MET A 469 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.918A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 518 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.677A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.808A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.598A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 820 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.760A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.662A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.588A pdb=" N LYS A 940 " --> pdb=" O ASP A 937 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 943 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.542A pdb=" N THR A1038 " --> pdb=" O GLN A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.690A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1101 removed outlier: 3.585A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A1093 " --> pdb=" O ALA A1089 " (cutoff:3.500A) Proline residue: A1098 - end of helix removed outlier: 3.553A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.507A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1189 through 1196 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1296 Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1387 removed outlier: 7.590A pdb=" N ILE A1371 " --> pdb=" O THR A1367 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N GLU A1372 " --> pdb=" O VAL A1368 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1373 " --> pdb=" O LEU A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.969A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.800A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 removed outlier: 3.677A pdb=" N LYS A1429 " --> pdb=" O GLY A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1446 removed outlier: 3.644A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1461 removed outlier: 3.515A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1484 Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.589A pdb=" N CYS B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.706A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 4.627A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 309 removed outlier: 3.660A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 332 through 346 Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 378 removed outlier: 3.824A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.824A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.868A pdb=" N ILE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 removed outlier: 4.071A pdb=" N THR B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.830A pdb=" N GLU B 600 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 646 removed outlier: 3.667A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 678 through 685 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.592A pdb=" N MET B 702 " --> pdb=" O HIS B 699 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.555A pdb=" N ASN B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 978 through 994 removed outlier: 3.671A pdb=" N CYS B 984 " --> pdb=" O HIS B 980 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 985 " --> pdb=" O LEU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1019 Processing helix chain 'B' and resid 1054 through 1059 removed outlier: 3.605A pdb=" N LYS B1058 " --> pdb=" O MET B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1107 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.588A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.622A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 269 removed outlier: 3.573A pdb=" N ILE C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 4.165A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 52 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.716A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 122 removed outlier: 3.616A pdb=" N ALA E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.551A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.693A pdb=" N GLY H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.618A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.504A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.991A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.108A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.892A pdb=" N GLU M 51 " --> pdb=" O ASP M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 128 removed outlier: 3.725A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 removed outlier: 3.531A pdb=" N LYS M 149 " --> pdb=" O VAL M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.525A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 202 Processing helix chain 'M' and resid 211 through 222 removed outlier: 4.085A pdb=" N SER M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG M 217 " --> pdb=" O ASP M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 242 Processing helix chain 'M' and resid 249 through 264 Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'M' and resid 295 through 300 removed outlier: 3.680A pdb=" N LEU M 299 " --> pdb=" O ARG M 295 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 295 through 300' Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'N' and resid 10 through 33 removed outlier: 4.355A pdb=" N ASP N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE N 28 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 51 Processing helix chain 'N' and resid 307 through 311 Processing helix chain 'N' and resid 312 through 318 removed outlier: 4.212A pdb=" N ASN N 315 " --> pdb=" O GLU N 312 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU N 317 " --> pdb=" O LEU N 314 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP N 318 " --> pdb=" O ASN N 315 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 8 removed outlier: 3.975A pdb=" N TYR O 6 " --> pdb=" O TYR O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 25 Processing helix chain 'O' and resid 29 through 51 Processing helix chain 'P' and resid 153 through 160 removed outlier: 6.264A pdb=" N SER P 158 " --> pdb=" O ALA P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 187 Processing helix chain 'P' and resid 226 through 244 Processing helix chain 'P' and resid 269 through 277 Processing helix chain 'P' and resid 317 through 334 removed outlier: 3.580A pdb=" N ILE P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Proline residue: P 330 - end of helix Processing helix chain 'Q' and resid 12 through 25 Processing helix chain 'Q' and resid 27 through 40 removed outlier: 4.305A pdb=" N ALA Q 33 " --> pdb=" O GLU Q 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE Q 36 " --> pdb=" O LEU Q 32 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Q 40 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 53 Processing helix chain 'Q' and resid 55 through 70 Processing helix chain 'Q' and resid 102 through 119 Processing helix chain 'Q' and resid 137 through 144 removed outlier: 4.054A pdb=" N ASN Q 142 " --> pdb=" O ASP Q 138 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 188 Proline residue: Q 186 - end of helix Processing helix chain 'Q' and resid 188 through 204 Processing helix chain 'R' and resid 76 through 92 Processing helix chain 'R' and resid 98 through 106 Processing helix chain 'R' and resid 108 through 111 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'R' and resid 151 through 157 removed outlier: 3.890A pdb=" N GLN R 157 " --> pdb=" O ARG R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 174 removed outlier: 4.203A pdb=" N ALA R 174 " --> pdb=" O ASP R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 185 removed outlier: 4.630A pdb=" N LYS R 180 " --> pdb=" O PRO R 176 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 221 Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'S' and resid 104 through 107 Processing helix chain 'S' and resid 160 through 168 Processing helix chain 'S' and resid 173 through 180 removed outlier: 4.244A pdb=" N MET S 177 " --> pdb=" O HIS S 173 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG S 180 " --> pdb=" O ILE S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 5 Processing helix chain 'T' and resid 9 through 15 Processing helix chain 'T' and resid 25 through 33 removed outlier: 3.584A pdb=" N LYS T 33 " --> pdb=" O GLN T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 137 removed outlier: 3.602A pdb=" N LEU T 127 " --> pdb=" O ASN T 123 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS T 137 " --> pdb=" O GLU T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 169 Processing helix chain 'T' and resid 179 through 194 removed outlier: 3.606A pdb=" N LYS T 193 " --> pdb=" O SER T 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS T 194 " --> pdb=" O ALA T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 207 Processing helix chain 'T' and resid 209 through 221 Processing helix chain 'U' and resid 138 through 153 Processing helix chain 'U' and resid 156 through 162 removed outlier: 3.740A pdb=" N ALA U 160 " --> pdb=" O ASP U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 181 Processing helix chain 'U' and resid 184 through 199 Processing helix chain 'U' and resid 203 through 212 removed outlier: 4.298A pdb=" N ARG U 207 " --> pdb=" O ASN U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 216 through 221 Processing helix chain 'U' and resid 232 through 248 Processing helix chain 'U' and resid 292 through 295 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 4.088A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 10.616A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AA5, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.902A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.118A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.738A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.459A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG H 57 " --> pdb=" O LYS H 146 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.658A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.533A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 901 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1139 through 1142 removed outlier: 3.547A pdb=" N MET A1309 " --> pdb=" O GLU A1337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1163 through 1165 removed outlier: 4.438A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A1298 " --> pdb=" O THR A1164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 4.208A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1321 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.715A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC3, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.223A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 205 through 209 removed outlier: 6.561A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC7, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC8, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.132A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.762A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 926 " --> pdb=" O THR B 901 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N THR B 901 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 5.427A pdb=" N VAL B 794 " --> pdb=" O CYS B 945 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 947 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 826 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.687A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD6, first strand: chain 'C' and resid 9 through 14 removed outlier: 5.420A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.748A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.766A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.320A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.596A pdb=" N VAL E 106 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.787A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN G 91 " --> pdb=" O PHE G 98 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AE7, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE8, first strand: chain 'I' and resid 80 through 81 removed outlier: 3.790A pdb=" N ALA I 94 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 24 through 25 Processing sheet with id=AF2, first strand: chain 'N' and resid 363 through 366 removed outlier: 5.560A pdb=" N LYS N 354 " --> pdb=" O TYR N 339 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR N 339 " --> pdb=" O LYS N 354 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY N 356 " --> pdb=" O CYS N 337 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS N 337 " --> pdb=" O GLY N 356 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N MET N 358 " --> pdb=" O VAL N 335 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL N 335 " --> pdb=" O MET N 358 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU N 360 " --> pdb=" O ASN N 333 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASN N 333 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS O 98 " --> pdb=" O CYS N 337 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU O 87 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG O 82 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS O 89 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU O 80 " --> pdb=" O LYS O 89 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP O 91 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP O 72 " --> pdb=" O PHE O 67 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE O 67 " --> pdb=" O TRP O 72 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE O 74 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR O 65 " --> pdb=" O PHE O 74 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU O 76 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASN O 63 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP O 78 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER O 61 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA P 190 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR O 65 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU P 165 " --> pdb=" O GLY P 260 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY P 260 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN P 167 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N MET P 258 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN P 173 " --> pdb=" O ASP P 252 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP P 252 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 363 through 366 removed outlier: 6.390A pdb=" N LYS N 369 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE O 58 " --> pdb=" O LYS N 369 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE N 371 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N GLY O 60 " --> pdb=" O ILE N 371 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP N 373 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU O 62 " --> pdb=" O ASP N 373 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU N 375 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR O 64 " --> pdb=" O GLU N 375 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA P 190 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR O 65 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU P 165 " --> pdb=" O GLY P 260 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY P 260 " --> pdb=" O LEU P 165 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN P 167 " --> pdb=" O MET P 258 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N MET P 258 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL P 169 " --> pdb=" O GLN P 256 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN P 173 " --> pdb=" O ASP P 252 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP P 252 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N MET P 258 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY P 314 " --> pdb=" O MET P 258 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 43 through 44 Processing sheet with id=AF5, first strand: chain 'Q' and resid 145 through 146 removed outlier: 3.531A pdb=" N THR Q 151 " --> pdb=" O ASP Q 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 131 through 133 Processing sheet with id=AF7, first strand: chain 'R' and resid 165 through 166 removed outlier: 4.101A pdb=" N GLY R 165 " --> pdb=" O PHE R 202 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE R 202 " --> pdb=" O GLY R 165 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 45 through 49 removed outlier: 6.760A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N GLN T 91 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL T 111 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU T 93 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE T 109 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL T 18 " --> pdb=" O GLN T 112 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ALA T 114 " --> pdb=" O VAL T 18 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU T 20 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS T 116 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS T 22 " --> pdb=" O CYS T 116 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N GLY T 17 " --> pdb=" O GLN S 129 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLN S 129 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE S 135 " --> pdb=" O GLU S 13 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL S 15 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA S 137 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG S 17 " --> pdb=" O ALA S 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY T 41 " --> pdb=" O VAL S 16 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG T 51 " --> pdb=" O THR T 48 " (cutoff:3.500A) removed outlier: 11.179A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 45 through 49 removed outlier: 6.760A pdb=" N TYR S 26 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR S 144 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE S 28 " --> pdb=" O TYR S 144 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE S 146 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ALA S 30 " --> pdb=" O PHE S 146 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N ASN S 32 " --> pdb=" O PRO S 148 " (cutoff:3.500A) removed outlier: 9.885A pdb=" N GLN T 91 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL T 111 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU T 93 " --> pdb=" O ILE T 109 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE T 109 " --> pdb=" O LEU T 93 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL T 95 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP T 8 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY T 108 " --> pdb=" O ASP T 8 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 197 through 198 Processing sheet with id=AG2, first strand: chain 'U' and resid 272 through 274 1999 hydrogen bonds defined for protein. 5493 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 254 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 27.31 Time building geometry restraints manager: 21.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 7817 1.30 - 1.45: 13975 1.45 - 1.60: 26628 1.60 - 1.75: 283 1.75 - 1.90: 423 Bond restraints: 49126 Sorted by residual: bond pdb=" CA ASN R 204 " pdb=" C ASN R 204 " ideal model delta sigma weight residual 1.522 1.614 -0.092 1.20e-02 6.94e+03 5.89e+01 bond pdb=" CA VAL A 521 " pdb=" CB VAL A 521 " ideal model delta sigma weight residual 1.537 1.574 -0.038 5.00e-03 4.00e+04 5.63e+01 bond pdb=" N ASN R 204 " pdb=" CA ASN R 204 " ideal model delta sigma weight residual 1.456 1.539 -0.083 1.16e-02 7.43e+03 5.14e+01 bond pdb=" CA CYS A1159 " pdb=" CB CYS A1159 " ideal model delta sigma weight residual 1.528 1.639 -0.110 1.59e-02 3.96e+03 4.83e+01 bond pdb=" C PHE A 482 " pdb=" O PHE A 482 " ideal model delta sigma weight residual 1.235 1.152 0.083 1.21e-02 6.83e+03 4.69e+01 ... (remaining 49121 not shown) Histogram of bond angle deviations from ideal: 57.05 - 73.25: 3 73.25 - 89.46: 5 89.46 - 105.66: 2039 105.66 - 121.87: 53834 121.87 - 138.07: 11129 Bond angle restraints: 67010 Sorted by residual: angle pdb=" N VAL Q 102 " pdb=" CA VAL Q 102 " pdb=" C VAL Q 102 " ideal model delta sigma weight residual 112.43 88.29 24.14 9.20e-01 1.18e+00 6.89e+02 angle pdb=" N LEU J 65 " pdb=" CA LEU J 65 " pdb=" C LEU J 65 " ideal model delta sigma weight residual 113.16 89.71 23.45 1.24e+00 6.50e-01 3.58e+02 angle pdb=" C HIS I 84 " pdb=" N PRO I 85 " pdb=" CD PRO I 85 " ideal model delta sigma weight residual 125.00 57.05 67.95 4.10e+00 5.95e-02 2.75e+02 angle pdb=" N ASP U 231 " pdb=" CA ASP U 231 " pdb=" C ASP U 231 " ideal model delta sigma weight residual 113.50 94.28 19.22 1.23e+00 6.61e-01 2.44e+02 angle pdb=" N SER B 882 " pdb=" CA SER B 882 " pdb=" C SER B 882 " ideal model delta sigma weight residual 111.81 90.04 21.77 1.44e+00 4.82e-01 2.29e+02 ... (remaining 67005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 28365 35.87 - 71.73: 1122 71.73 - 107.60: 80 107.60 - 143.46: 0 143.46 - 179.33: 7 Dihedral angle restraints: 29574 sinusoidal: 13315 harmonic: 16259 Sorted by residual: dihedral pdb=" CA TYR A1308 " pdb=" C TYR A1308 " pdb=" N MET A1309 " pdb=" CA MET A1309 " ideal model delta harmonic sigma weight residual 180.00 105.49 74.51 0 5.00e+00 4.00e-02 2.22e+02 dihedral pdb=" CA ILE N 371 " pdb=" C ILE N 371 " pdb=" N GLY N 372 " pdb=" CA GLY N 372 " ideal model delta harmonic sigma weight residual -180.00 -125.59 -54.41 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA ALA Q 125 " pdb=" C ALA Q 125 " pdb=" N SER Q 126 " pdb=" CA SER Q 126 " ideal model delta harmonic sigma weight residual 180.00 -129.47 -50.53 0 5.00e+00 4.00e-02 1.02e+02 ... (remaining 29571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 7247 0.191 - 0.383: 184 0.383 - 0.574: 21 0.574 - 0.766: 3 0.766 - 0.957: 1 Chirality restraints: 7456 Sorted by residual: chirality pdb=" CA LEU M 39 " pdb=" N LEU M 39 " pdb=" C LEU M 39 " pdb=" CB LEU M 39 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.29e+01 chirality pdb=" CA LEU R 163 " pdb=" N LEU R 163 " pdb=" C LEU R 163 " pdb=" CB LEU R 163 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA LEU B 880 " pdb=" N LEU B 880 " pdb=" C LEU B 880 " pdb=" CB LEU B 880 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 7453 not shown) Planarity restraints: 8154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 10 " -0.167 5.00e-02 4.00e+02 2.60e-01 1.08e+02 pdb=" N PRO M 11 " 0.445 5.00e-02 4.00e+02 pdb=" CA PRO M 11 " -0.190 5.00e-02 4.00e+02 pdb=" CD PRO M 11 " -0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 84 " 0.204 5.00e-02 4.00e+02 2.58e-01 1.07e+02 pdb=" N PRO I 85 " -0.431 5.00e-02 4.00e+02 pdb=" CA PRO I 85 " 0.196 5.00e-02 4.00e+02 pdb=" CD PRO I 85 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.156 5.00e-02 4.00e+02 2.35e-01 8.86e+01 pdb=" N PRO C 7 " 0.403 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.169 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.078 5.00e-02 4.00e+02 ... (remaining 8151 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 33 1.91 - 2.66: 1520 2.66 - 3.40: 65580 3.40 - 4.15: 114269 4.15 - 4.90: 199488 Nonbonded interactions: 380890 Sorted by model distance: nonbonded pdb=" C VAL A 264 " pdb=" ND2 ASN A 272 " model vdw 1.160 3.350 nonbonded pdb=" CE2 PHE Q 180 " pdb=" OD1 ASP R 213 " model vdw 1.174 3.340 nonbonded pdb=" N VAL A 265 " pdb=" ND2 ASN A 272 " model vdw 1.181 3.200 nonbonded pdb=" OH TYR Q 20 " pdb=" CA PHE R 210 " model vdw 1.239 3.470 nonbonded pdb=" O VAL R 225 " pdb=" N SER R 227 " model vdw 1.273 2.520 ... (remaining 380885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 11 6.06 5 P 158 5.49 5 Mg 2 5.21 5 S 270 5.16 5 C 29697 2.51 5 N 8418 2.21 5 O 9371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 15.620 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.380 Process input model: 144.430 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.141 49126 Z= 0.754 Angle : 1.763 67.954 67010 Z= 1.114 Chirality : 0.079 0.957 7456 Planarity : 0.013 0.260 8154 Dihedral : 17.185 179.329 19046 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 4.18 % Allowed : 8.18 % Favored : 87.64 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.10), residues: 5525 helix: -0.52 (0.10), residues: 1987 sheet: -0.62 (0.18), residues: 725 loop : -2.46 (0.11), residues: 2813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11050 Ramachandran restraints generated. 5525 Oldfield, 0 Emsley, 5525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2241 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 2052 time to evaluate : 5.156 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 outliers start: 189 outliers final: 55 residues processed: 2166 average time/residue: 0.6788 time to fit residues: 2334.1451 Evaluate side-chains 1344 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1289 time to evaluate : 5.292 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 55 outliers final: 1 residues processed: 55 average time/residue: 0.5488 time to fit residues: 60.2145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 477 optimal weight: 1.9990 chunk 428 optimal weight: 4.9990 chunk 237 optimal weight: 0.3980 chunk 146 optimal weight: 0.7980 chunk 288 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 chunk 442 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 chunk 269 optimal weight: 0.3980 chunk 329 optimal weight: 0.5980 chunk 513 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 152 ASN A 222 HIS A 272 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 459 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 620 HIS ** A 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 780 ASN A 989 ASN ** A1077 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1445 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 141 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 370 HIS B 390 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 260 GLN C 275 ASN D 43 HIS D 141 GLN E 64 HIS ** E 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN F 46 GLN F 49 GLN ** H 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 89 ASN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN M 148 GLN M 234 HIS ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 172 ASN T 144 GLN T 159 HIS T 198 ASN ** U 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 248 HIS ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.105 49126 Z= 0.304 Angle : 0.921 27.210 67010 Z= 0.476 Chirality : 0.049 0.450 7456 Planarity : 0.007 0.196 8154 Dihedral : 17.421 179.812 7693 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.11 % Favored : 90.77 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.11), residues: 5525 helix: 0.61 (0.11), residues: 2031 sheet: -0.36 (0.18), residues: 743 loop : -1.82 (0.11), residues: 2751 *********************** 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 1702 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1475 time to evaluate : 5.615 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 outliers start: 227 outliers final: 118 residues processed: 1598 average time/residue: 0.6251 time to fit residues: 1617.1370 Evaluate side-chains 1298 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1180 time to evaluate : 5.430 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 3 residues processed: 118 average time/residue: 0.4197 time to fit residues: 99.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 427 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 514 optimal weight: 20.0000 chunk 555 optimal weight: 8.9990 chunk 457 optimal weight: 0.5980 chunk 509 optimal weight: 0.4980 chunk 175 optimal weight: 6.9990 chunk 412 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 143 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 ASN A 780 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN A1077 ASN A1101 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN A1417 HIS B 90 GLN B 141 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN B 486 ASN B 525 ASN ** B 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1117 HIS C 134 ASN ** H 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN I 56 ASN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 89 ASN ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 ASN O 57 ASN P 189 ASN ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 ASN S 141 HIS T 144 GLN U 203 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 49126 Z= 0.318 Angle : 0.846 17.686 67010 Z= 0.437 Chirality : 0.047 0.345 7456 Planarity : 0.007 0.174 8154 Dihedral : 17.232 179.826 7693 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.36 % Favored : 90.73 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.11), residues: 5525 helix: 0.68 (0.11), residues: 2020 sheet: -0.33 (0.18), residues: 793 loop : -1.67 (0.12), residues: 2712 *********************** 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 1437 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1264 time to evaluate : 5.333 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 outliers start: 173 outliers final: 89 residues processed: 1366 average time/residue: 0.6341 time to fit residues: 1409.8797 Evaluate side-chains 1226 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1137 time to evaluate : 5.182 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 2 residues processed: 89 average time/residue: 0.4365 time to fit residues: 79.5950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 507 optimal weight: 6.9990 chunk 386 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 345 optimal weight: 40.0000 chunk 515 optimal weight: 30.0000 chunk 546 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 488 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 210 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 333 ASN O 4 GLN O 45 ASN ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** T 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 239 ASN U 257 GLN U 270 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 49126 Z= 0.400 Angle : 0.856 19.716 67010 Z= 0.441 Chirality : 0.048 0.336 7456 Planarity : 0.007 0.168 8154 Dihedral : 17.212 179.926 7693 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.85 % Allowed : 8.60 % Favored : 90.55 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.61 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 5525 helix: 0.59 (0.11), residues: 2010 sheet: -0.54 (0.17), residues: 802 loop : -1.71 (0.12), residues: 2713 *********************** 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 1353 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1189 time to evaluate : 5.540 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 outliers start: 164 outliers final: 102 residues processed: 1285 average time/residue: 0.6190 time to fit residues: 1293.6976 Evaluate side-chains 1188 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1086 time to evaluate : 5.328 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 102 outliers final: 3 residues processed: 102 average time/residue: 0.4524 time to fit residues: 91.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 454 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 406 optimal weight: 0.6980 chunk 225 optimal weight: 0.7980 chunk 466 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 490 optimal weight: 0.0000 chunk 137 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A 982 ASN A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 319 ASN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 129 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 49126 Z= 0.257 Angle : 0.809 16.998 67010 Z= 0.414 Chirality : 0.046 0.312 7456 Planarity : 0.006 0.157 8154 Dihedral : 17.116 179.155 7693 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.84 % Favored : 91.44 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 1.21 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.11), residues: 5525 helix: 0.66 (0.11), residues: 2014 sheet: -0.44 (0.18), residues: 822 loop : -1.62 (0.12), residues: 2689 *********************** 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 1319 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1228 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 48 residues processed: 1272 average time/residue: 0.6681 time to fit residues: 1391.7773 Evaluate side-chains 1141 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1093 time to evaluate : 5.330 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 48 outliers final: 2 residues processed: 48 average time/residue: 0.4579 time to fit residues: 48.0406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 183 optimal weight: 0.7980 chunk 491 optimal weight: 9.9990 chunk 107 optimal weight: 0.4980 chunk 320 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 546 optimal weight: 0.9990 chunk 453 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN B 245 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN B 537 GLN ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 49126 Z= 0.254 Angle : 0.827 20.288 67010 Z= 0.420 Chirality : 0.046 0.297 7456 Planarity : 0.006 0.180 8154 Dihedral : 17.048 178.778 7693 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.82 % Favored : 91.49 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -0.87 (0.11), residues: 5525 helix: 0.63 (0.12), residues: 2012 sheet: -0.41 (0.18), residues: 822 loop : -1.60 (0.12), residues: 2691 *********************** 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 1298 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1191 time to evaluate : 5.240 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 outliers start: 107 outliers final: 76 residues processed: 1239 average time/residue: 0.6460 time to fit residues: 1300.4630 Evaluate side-chains 1177 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1101 time to evaluate : 5.158 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 76 outliers final: 2 residues processed: 76 average time/residue: 0.4655 time to fit residues: 71.0038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 527 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 311 optimal weight: 0.2980 chunk 399 optimal weight: 8.9990 chunk 309 optimal weight: 0.7980 chunk 460 optimal weight: 0.9980 chunk 305 optimal weight: 2.9990 chunk 544 optimal weight: 0.5980 chunk 340 optimal weight: 9.9990 chunk 332 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN G 155 ASN H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** L 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 239 ASN ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 49126 Z= 0.241 Angle : 0.838 18.385 67010 Z= 0.424 Chirality : 0.046 0.298 7456 Planarity : 0.006 0.176 8154 Dihedral : 17.045 178.228 7693 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.86 % Favored : 91.53 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -0.85 (0.11), residues: 5525 helix: 0.60 (0.12), residues: 2011 sheet: -0.36 (0.17), residues: 838 loop : -1.55 (0.12), residues: 2676 *********************** 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 1267 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1191 time to evaluate : 5.705 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 outliers start: 76 outliers final: 41 residues processed: 1222 average time/residue: 0.6202 time to fit residues: 1243.2274 Evaluate side-chains 1144 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1103 time to evaluate : 5.810 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 2 residues processed: 41 average time/residue: 0.4445 time to fit residues: 42.2434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 336 optimal weight: 4.9990 chunk 217 optimal weight: 0.3980 chunk 325 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 428 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 390 ASN B 631 GLN B 722 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 126 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 164 GLN ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** U 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 49126 Z= 0.349 Angle : 0.877 17.658 67010 Z= 0.446 Chirality : 0.047 0.313 7456 Planarity : 0.006 0.142 8154 Dihedral : 17.060 178.589 7693 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.40 % Favored : 90.97 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -0.99 (0.11), residues: 5525 helix: 0.47 (0.12), residues: 2016 sheet: -0.42 (0.17), residues: 838 loop : -1.64 (0.12), residues: 2671 *********************** 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 1214 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1121 time to evaluate : 5.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 59 residues processed: 1156 average time/residue: 0.6150 time to fit residues: 1160.6998 Evaluate side-chains 1129 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1070 time to evaluate : 5.331 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 59 outliers final: 2 residues processed: 59 average time/residue: 0.4670 time to fit residues: 58.5574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 495 optimal weight: 0.9990 chunk 521 optimal weight: 0.1980 chunk 475 optimal weight: 10.0000 chunk 507 optimal weight: 7.9990 chunk 305 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 chunk 398 optimal weight: 0.0050 chunk 155 optimal weight: 0.9990 chunk 458 optimal weight: 0.9990 chunk 479 optimal weight: 0.9980 chunk 505 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN G 155 ASN H 46 GLN ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 197 ASN ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 49126 Z= 0.255 Angle : 0.883 17.275 67010 Z= 0.446 Chirality : 0.047 0.538 7456 Planarity : 0.006 0.138 8154 Dihedral : 17.031 177.775 7693 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.96 % Favored : 91.40 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -0.97 (0.11), residues: 5525 helix: 0.48 (0.12), residues: 2000 sheet: -0.45 (0.17), residues: 868 loop : -1.59 (0.12), residues: 2657 *********************** 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 1190 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1161 time to evaluate : 5.390 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 outliers start: 29 outliers final: 18 residues processed: 1173 average time/residue: 0.6407 time to fit residues: 1228.2272 Evaluate side-chains 1102 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1084 time to evaluate : 5.421 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.4243 time to fit residues: 21.9219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 333 optimal weight: 4.9990 chunk 536 optimal weight: 0.9980 chunk 327 optimal weight: 0.9990 chunk 254 optimal weight: 0.4980 chunk 373 optimal weight: 0.7980 chunk 562 optimal weight: 6.9990 chunk 518 optimal weight: 10.0000 chunk 448 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 346 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 ASN ** A1220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 370 HIS B 390 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN ** G 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 49126 Z= 0.281 Angle : 0.903 18.103 67010 Z= 0.455 Chirality : 0.048 0.401 7456 Planarity : 0.006 0.134 8154 Dihedral : 16.979 177.606 7693 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.34 % Favored : 91.02 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.11), residues: 5525 helix: 0.43 (0.12), residues: 2006 sheet: -0.46 (0.17), residues: 851 loop : -1.62 (0.12), residues: 2668 ********************** 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 1152 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1114 time to evaluate : 5.708 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 outliers start: 38 outliers final: 25 residues processed: 1132 average time/residue: 0.6519 time to fit residues: 1215.4912 Evaluate side-chains 1104 residues out of total 4932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1079 time to evaluate : 7.291 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.4403 time to fit residues: 29.4046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 565 random chunks: chunk 356 optimal weight: 0.0670 chunk 477 optimal weight: 40.0000 chunk 137 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 448 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 460 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A1024 ASN ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN H 46 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.174398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127554 restraints weight = 91773.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123756 restraints weight = 86958.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125173 restraints weight = 91088.054| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 49126 Z= 0.288 Angle : 0.900 19.397 67010 Z= 0.455 Chirality : 0.047 0.368 7456 Planarity : 0.006 0.131 8154 Dihedral : 16.951 177.369 7693 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.33 % Favored : 91.04 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.02 % Twisted Proline : 0.40 % 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: -1.05 (0.11), residues: 5525 helix: 0.39 (0.12), residues: 2014 sheet: -0.43 (0.17), residues: 847 loop : -1.65 (0.12), residues: 2664 =============================================================================== Job complete usr+sys time: 18601.48 seconds wall clock time: 328 minutes 40.09 seconds (19720.09 seconds total)