Starting phenix.real_space_refine on Tue Feb 20 00:01:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtd_33447/02_2024/7xtd_33447.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtd_33447/02_2024/7xtd_33447.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/7xtd_33447/02_2024/7xtd_33447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtd_33447/02_2024/7xtd_33447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtd_33447/02_2024/7xtd_33447.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtd_33447/02_2024/7xtd_33447.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 254 5.49 5 Mg 1 5.21 5 S 317 5.16 5 C 50780 2.51 5 N 14319 2.21 5 O 15987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 81668 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1404, 11064 Classifications: {'peptide': 1404} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9284 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 52, 'TRANS': 1111} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1349 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1741 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1325 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "N" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2305 Classifications: {'DNA': 112} Link IDs: {'rna3p': 111} Chain breaks: 1 Chain: "P" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain: "T" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2512 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "W" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4232 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Chain: "m" Number of atoms: 9730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9730 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "n" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "q" Number of atoms: 7552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7552 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 910} Chain: "r" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2139 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 2 Chain: "u" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1707 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "v" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2878 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 22, 'TRANS': 326} Chain breaks: 3 Chain: "x" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "a" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 735 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 544 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "j" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3780 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "k" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3502 Classifications: {'peptide': 429} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 409} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" 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 527 SG CYS A 67 143.776 92.136 83.858 1.00114.08 S ATOM 549 SG CYS A 70 147.390 91.092 84.448 1.00 99.79 S ATOM 594 SG CYS A 77 146.313 94.687 85.150 1.00 85.01 S ATOM 829 SG CYS A 107 145.941 116.802 42.213 1.00177.50 S ATOM 851 SG CYS A 110 147.934 113.778 41.045 1.00199.94 S ATOM 1157 SG CYS A 148 148.177 117.046 39.195 1.00265.61 S ATOM 1229 SG CYS A 168 144.791 115.135 39.181 1.00279.84 S ATOM 19880 SG CYS B1163 157.202 92.325 70.945 1.00 82.09 S ATOM 19898 SG CYS B1166 155.204 95.491 70.591 1.00 83.79 S ATOM 20021 SG CYS B1182 153.405 92.204 71.298 1.00 99.94 S ATOM 20044 SG CYS B1185 155.014 92.935 67.881 1.00 93.95 S ATOM 20989 SG CYS C 85 159.058 104.442 151.051 1.00147.36 S ATOM 21002 SG CYS C 87 155.682 103.198 149.841 1.00173.36 S ATOM 21037 SG CYS C 91 155.863 105.085 152.950 1.00126.84 S ATOM 21060 SG CYS C 94 156.557 107.061 149.833 1.00110.62 S ATOM 29206 SG CYS I 78 148.878 197.735 94.362 1.00418.44 S ATOM 29422 SG CYS I 103 149.669 193.370 93.789 1.00395.33 S ATOM 28659 SG CYS I 10 126.056 176.742 54.888 1.00295.05 S ATOM 28822 SG CYS I 29 129.999 177.267 52.665 1.00302.33 S ATOM 28847 SG CYS I 32 128.138 178.906 52.083 1.00289.80 S ATOM 29563 SG CYS J 7 159.243 137.777 139.748 1.00 56.50 S ATOM 29586 SG CYS J 10 161.990 136.977 142.349 1.00 59.04 S ATOM 29862 SG CYS J 44 162.307 139.989 139.928 1.00 63.81 S ATOM 29868 SG CYS J 45 160.015 139.903 142.914 1.00 63.28 S ATOM 31039 SG CYS L 33 119.070 122.829 128.726 1.00113.54 S ATOM 31054 SG CYS L 36 117.252 123.328 131.852 1.00135.53 S ATOM 31164 SG CYS L 50 116.212 120.492 129.656 1.00124.15 S ATOM 31188 SG CYS L 53 115.560 123.861 128.795 1.00153.45 S ATOM 31445 SG CYS M 25 118.381 138.736 44.447 1.00429.47 S ATOM 31470 SG CYS M 28 118.596 135.005 44.618 1.00437.35 S ATOM 31628 SG CYS M 49 121.475 136.948 43.065 1.00431.39 S ATOM 31652 SG CYS M 52 117.996 136.570 41.315 1.00442.26 S ATOM 37116 SG CYS V 12 90.473 106.138 58.422 1.00419.10 S ATOM 37138 SG CYS V 15 91.490 109.236 56.643 1.00406.78 S ATOM 37240 SG CYS V 29 87.961 109.064 57.520 1.00400.07 S ATOM 37261 SG CYS V 32 89.268 106.821 54.787 1.00424.36 S Time building chain proxies: 33.07, per 1000 atoms: 0.40 Number of scatterers: 81668 At special positions: 0 Unit cell: (280.476, 221.116, 203.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 317 16.00 P 254 15.00 Mg 1 11.99 O 15987 8.00 N 14319 7.00 C 50780 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: 27.14 Conformation dependent library (CDL) restraints added in 10.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " Number of angles added : 45 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18034 Finding SS restraints... Secondary structure from input PDB file: 370 helices and 88 sheets defined 47.8% alpha, 15.1% beta 111 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 23.01 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.723A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.527A pdb=" N THR A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.702A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.710A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.525A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.890A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.678A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.505A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.768A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.582A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.726A pdb=" N ILE A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.616A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.729A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 924 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.683A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.570A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.624A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.635A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.986A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.513A pdb=" N SER A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.811A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1451 through 1455 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.662A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 314 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.648A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 430 removed outlier: 4.198A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.619A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 removed outlier: 3.645A pdb=" N ALA B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.207A pdb=" N ARG B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.346A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.576A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.500A pdb=" N GLU B 696 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.620A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.746A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.552A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.535A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.507A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 921 through 926 removed outlier: 4.145A pdb=" N GLU B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 926 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 removed outlier: 3.654A pdb=" N MET B 999 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.632A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.961A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.532A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.609A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.979A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.994A pdb=" N THR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 131 removed outlier: 3.605A pdb=" N SER D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.670A pdb=" N VAL D 136 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.714A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.193A pdb=" N ALA D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 166' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.588A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.586A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.639A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.708A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.528A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.571A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.891A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.818A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'V' and resid 20 through 28 Processing helix chain 'V' and resid 31 through 35 removed outlier: 4.047A pdb=" N SER V 34 " --> pdb=" O ASN V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 Processing helix chain 'W' and resid 304 through 310 removed outlier: 4.208A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 452 Processing helix chain 'W' and resid 453 through 455 No H-bonds generated for 'chain 'W' and resid 453 through 455' Processing helix chain 'W' and resid 461 through 475 Processing helix chain 'W' and resid 515 through 520 Processing helix chain 'W' and resid 692 through 695 Processing helix chain 'W' and resid 760 through 764 removed outlier: 4.298A pdb=" N TYR W 763 " --> pdb=" O GLN W 760 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS W 764 " --> pdb=" O GLY W 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 760 through 764' Processing helix chain 'W' and resid 792 through 794 No H-bonds generated for 'chain 'W' and resid 792 through 794' Processing helix chain 'm' and resid 230 through 242 Processing helix chain 'm' and resid 244 through 259 removed outlier: 4.416A pdb=" N TRP m 249 " --> pdb=" O THR m 245 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N THR m 250 " --> pdb=" O ASP m 246 " (cutoff:3.500A) Processing helix chain 'm' and resid 279 through 284 Processing helix chain 'm' and resid 285 through 293 Processing helix chain 'm' and resid 295 through 304 Processing helix chain 'm' and resid 307 through 314 Processing helix chain 'm' and resid 323 through 342 Processing helix chain 'm' and resid 342 through 353 Processing helix chain 'm' and resid 358 through 377 Processing helix chain 'm' and resid 380 through 388 Processing helix chain 'm' and resid 388 through 393 removed outlier: 3.934A pdb=" N ALA m 392 " --> pdb=" O ARG m 388 " (cutoff:3.500A) Processing helix chain 'm' and resid 410 through 442 removed outlier: 3.944A pdb=" N ASP m 429 " --> pdb=" O HIS m 425 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS m 430 " --> pdb=" O SER m 426 " (cutoff:3.500A) Processing helix chain 'm' and resid 447 through 456 removed outlier: 3.603A pdb=" N SER m 456 " --> pdb=" O GLU m 452 " (cutoff:3.500A) Processing helix chain 'm' and resid 459 through 474 Processing helix chain 'm' and resid 474 through 484 Processing helix chain 'm' and resid 518 through 527 Processing helix chain 'm' and resid 529 through 537 removed outlier: 4.044A pdb=" N ALA m 537 " --> pdb=" O VAL m 533 " (cutoff:3.500A) Processing helix chain 'm' and resid 538 through 549 Processing helix chain 'm' and resid 561 through 573 Processing helix chain 'm' and resid 581 through 599 Processing helix chain 'm' and resid 600 through 615 removed outlier: 3.503A pdb=" N ARG m 604 " --> pdb=" O GLU m 600 " (cutoff:3.500A) Processing helix chain 'm' and resid 622 through 629 removed outlier: 3.521A pdb=" N ILE m 629 " --> pdb=" O GLY m 625 " (cutoff:3.500A) Processing helix chain 'm' and resid 633 through 639 removed outlier: 3.718A pdb=" N ASP m 637 " --> pdb=" O PRO m 634 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS m 639 " --> pdb=" O PHE m 636 " (cutoff:3.500A) Processing helix chain 'm' and resid 648 through 651 Processing helix chain 'm' and resid 652 through 665 removed outlier: 3.909A pdb=" N TYR m 656 " --> pdb=" O THR m 652 " (cutoff:3.500A) Processing helix chain 'm' and resid 676 through 689 Processing helix chain 'm' and resid 694 through 748 Proline residue: m 717 - end of helix Processing helix chain 'm' and resid 802 through 815 removed outlier: 3.567A pdb=" N SER m 806 " --> pdb=" O SER m 802 " (cutoff:3.500A) Processing helix chain 'm' and resid 830 through 847 removed outlier: 4.059A pdb=" N LYS m 834 " --> pdb=" O ILE m 830 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU m 835 " --> pdb=" O HIS m 831 " (cutoff:3.500A) Processing helix chain 'm' and resid 878 through 887 removed outlier: 3.749A pdb=" N HIS m 886 " --> pdb=" O ARG m 882 " (cutoff:3.500A) Processing helix chain 'm' and resid 887 through 894 removed outlier: 3.688A pdb=" N SER m 891 " --> pdb=" O SER m 887 " (cutoff:3.500A) Processing helix chain 'm' and resid 898 through 913 Processing helix chain 'm' and resid 913 through 921 Processing helix chain 'm' and resid 922 through 928 removed outlier: 4.125A pdb=" N MET m 925 " --> pdb=" O ASP m 922 " (cutoff:3.500A) Processing helix chain 'm' and resid 938 through 958 Processing helix chain 'm' and resid 961 through 967 Processing helix chain 'm' and resid 967 through 972 Processing helix chain 'm' and resid 973 through 977 Processing helix chain 'm' and resid 981 through 996 Processing helix chain 'm' and resid 1003 through 1008 Processing helix chain 'm' and resid 1012 through 1020 Processing helix chain 'm' and resid 1030 through 1034 removed outlier: 3.951A pdb=" N ARG m1033 " --> pdb=" O ASP m1030 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN m1034 " --> pdb=" O VAL m1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1030 through 1034' Processing helix chain 'm' and resid 1040 through 1045 Processing helix chain 'm' and resid 1048 through 1050 No H-bonds generated for 'chain 'm' and resid 1048 through 1050' Processing helix chain 'm' and resid 1051 through 1064 Processing helix chain 'm' and resid 1072 through 1085 Processing helix chain 'm' and resid 1097 through 1103 Processing helix chain 'm' and resid 1104 through 1117 removed outlier: 3.558A pdb=" N TYR m1108 " --> pdb=" O ILE m1104 " (cutoff:3.500A) Processing helix chain 'm' and resid 1120 through 1133 Processing helix chain 'm' and resid 1146 through 1156 Processing helix chain 'm' and resid 1194 through 1198 removed outlier: 4.377A pdb=" N LEU m1198 " --> pdb=" O ARG m1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1194 through 1198' Processing helix chain 'm' and resid 1205 through 1210 Processing helix chain 'm' and resid 1235 through 1240 Processing helix chain 'm' and resid 1256 through 1273 Processing helix chain 'm' and resid 1290 through 1300 removed outlier: 3.706A pdb=" N ALA m1300 " --> pdb=" O ASP m1296 " (cutoff:3.500A) Processing helix chain 'm' and resid 1358 through 1380 removed outlier: 3.930A pdb=" N ASN m1368 " --> pdb=" O VAL m1364 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN m1369 " --> pdb=" O GLU m1365 " (cutoff:3.500A) Processing helix chain 'm' and resid 1387 through 1402 Processing helix chain 'm' and resid 1453 through 1469 Processing helix chain 'n' and resid 153 through 180 Processing helix chain 'n' and resid 185 through 200 Proline residue: n 192 - end of helix removed outlier: 3.550A pdb=" N ARG n 200 " --> pdb=" O ASP n 196 " (cutoff:3.500A) Processing helix chain 'n' and resid 203 through 211 Processing helix chain 'n' and resid 212 through 221 Processing helix chain 'n' and resid 230 through 244 Processing helix chain 'n' and resid 247 through 255 Processing helix chain 'n' and resid 255 through 266 removed outlier: 4.551A pdb=" N VAL n 259 " --> pdb=" O GLY n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 270 through 289 Proline residue: n 287 - end of helix Processing helix chain 'q' and resid 5 through 13 removed outlier: 3.879A pdb=" N TYR q 9 " --> pdb=" O ASP q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 20 removed outlier: 3.750A pdb=" N GLU q 20 " --> pdb=" O ASP q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 23 No H-bonds generated for 'chain 'q' and resid 21 through 23' Processing helix chain 'q' and resid 46 through 58 Processing helix chain 'q' and resid 60 through 74 removed outlier: 3.663A pdb=" N TRP q 64 " --> pdb=" O ARG q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 89 Processing helix chain 'q' and resid 90 through 96 Processing helix chain 'q' and resid 97 through 120 removed outlier: 3.872A pdb=" N THR q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR q 119 " --> pdb=" O GLU q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 122 through 141 Processing helix chain 'q' and resid 144 through 158 removed outlier: 3.690A pdb=" N GLY q 148 " --> pdb=" O LEU q 144 " (cutoff:3.500A) Processing helix chain 'q' and resid 160 through 175 Processing helix chain 'q' and resid 178 through 192 Processing helix chain 'q' and resid 194 through 209 removed outlier: 3.535A pdb=" N LEU q 201 " --> pdb=" O GLN q 197 " (cutoff:3.500A) Processing helix chain 'q' and resid 215 through 227 removed outlier: 4.128A pdb=" N GLY q 219 " --> pdb=" O ASP q 215 " (cutoff:3.500A) Processing helix chain 'q' and resid 229 through 244 Processing helix chain 'q' and resid 248 through 267 removed outlier: 3.878A pdb=" N LYS q 252 " --> pdb=" O ASN q 248 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER q 267 " --> pdb=" O CYS q 263 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 289 Processing helix chain 'q' and resid 294 through 308 removed outlier: 3.601A pdb=" N SER q 303 " --> pdb=" O MET q 299 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR q 304 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing helix chain 'q' and resid 310 through 325 Processing helix chain 'q' and resid 328 through 347 removed outlier: 3.554A pdb=" N VAL q 332 " --> pdb=" O ASN q 328 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS q 345 " --> pdb=" O ARG q 341 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS q 346 " --> pdb=" O VAL q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 348 through 363 Processing helix chain 'q' and resid 366 through 380 removed outlier: 3.543A pdb=" N LYS q 370 " --> pdb=" O ASN q 366 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 397 Processing helix chain 'q' and resid 402 through 417 Processing helix chain 'q' and resid 419 through 438 Processing helix chain 'q' and resid 442 through 454 removed outlier: 3.803A pdb=" N TYR q 446 " --> pdb=" O LEU q 442 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 473 Processing helix chain 'q' and resid 474 through 476 No H-bonds generated for 'chain 'q' and resid 474 through 476' Processing helix chain 'q' and resid 477 through 491 Processing helix chain 'q' and resid 493 through 508 Processing helix chain 'q' and resid 509 through 511 No H-bonds generated for 'chain 'q' and resid 509 through 511' Processing helix chain 'q' and resid 512 through 535 removed outlier: 4.231A pdb=" N GLU q 517 " --> pdb=" O PRO q 513 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA q 518 " --> pdb=" O GLN q 514 " (cutoff:3.500A) Processing helix chain 'q' and resid 535 through 550 removed outlier: 3.533A pdb=" N ALA q 539 " --> pdb=" O ASN q 535 " (cutoff:3.500A) Processing helix chain 'q' and resid 553 through 569 removed outlier: 4.099A pdb=" N LYS q 557 " --> pdb=" O TYR q 553 " (cutoff:3.500A) Processing helix chain 'q' and resid 572 through 583 Processing helix chain 'q' and resid 586 through 605 removed outlier: 6.253A pdb=" N ARG q 602 " --> pdb=" O LYS q 598 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS q 603 " --> pdb=" O ARG q 599 " (cutoff:3.500A) Processing helix chain 'q' and resid 609 through 622 Processing helix chain 'q' and resid 626 through 644 Processing helix chain 'q' and resid 648 through 673 Processing helix chain 'q' and resid 676 through 690 removed outlier: 3.546A pdb=" N ALA q 680 " --> pdb=" O ASN q 676 " (cutoff:3.500A) Processing helix chain 'q' and resid 692 through 707 Processing helix chain 'q' and resid 709 through 723 Processing helix chain 'q' and resid 725 through 740 Processing helix chain 'q' and resid 745 through 764 removed outlier: 3.790A pdb=" N LEU q 749 " --> pdb=" O ASP q 745 " (cutoff:3.500A) Processing helix chain 'q' and resid 765 through 784 removed outlier: 3.672A pdb=" N TYR q 769 " --> pdb=" O SER q 765 " (cutoff:3.500A) Processing helix chain 'q' and resid 785 through 806 Processing helix chain 'q' and resid 807 through 811 Processing helix chain 'q' and resid 812 through 835 Processing helix chain 'q' and resid 842 through 856 removed outlier: 3.533A pdb=" N THR q 856 " --> pdb=" O MET q 852 " (cutoff:3.500A) Processing helix chain 'q' and resid 856 through 930 removed outlier: 3.778A pdb=" N ARG q 883 " --> pdb=" O LEU q 879 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG q 884 " --> pdb=" O ARG q 880 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS q 885 " --> pdb=" O THR q 881 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU q 917 " --> pdb=" O ILE q 913 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU q 918 " --> pdb=" O LYS q 914 " (cutoff:3.500A) Processing helix chain 'r' and resid 197 through 204 removed outlier: 3.801A pdb=" N ILE r 204 " --> pdb=" O ASP r 200 " (cutoff:3.500A) Processing helix chain 'r' and resid 207 through 215 Processing helix chain 'r' and resid 219 through 225 Processing helix chain 'r' and resid 287 through 289 No H-bonds generated for 'chain 'r' and resid 287 through 289' Processing helix chain 'r' and resid 295 through 310 Processing helix chain 'r' and resid 315 through 332 Processing helix chain 'r' and resid 335 through 350 Processing helix chain 'r' and resid 353 through 374 removed outlier: 3.658A pdb=" N VAL r 358 " --> pdb=" O GLY r 354 " (cutoff:3.500A) Processing helix chain 'r' and resid 378 through 391 removed outlier: 3.611A pdb=" N ARG r 382 " --> pdb=" O GLU r 378 " (cutoff:3.500A) Processing helix chain 'r' and resid 398 through 433 removed outlier: 3.827A pdb=" N ARG r 420 " --> pdb=" O ASN r 416 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU r 428 " --> pdb=" O MET r 424 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS r 429 " --> pdb=" O ALA r 425 " (cutoff:3.500A) Processing helix chain 'r' and resid 486 through 490 Processing helix chain 'r' and resid 492 through 497 Processing helix chain 'r' and resid 498 through 505 Processing helix chain 'u' and resid 122 through 129 Processing helix chain 'u' and resid 135 through 149 Processing helix chain 'u' and resid 228 through 242 removed outlier: 3.625A pdb=" N GLN u 242 " --> pdb=" O LEU u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 258 through 282 Processing helix chain 'v' and resid 32 through 35 Processing helix chain 'v' and resid 36 through 45 Processing helix chain 'v' and resid 47 through 58 Processing helix chain 'v' and resid 64 through 71 removed outlier: 3.573A pdb=" N ASP v 68 " --> pdb=" O GLU v 65 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY v 69 " --> pdb=" O THR v 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP v 71 " --> pdb=" O ASP v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 73 through 77 removed outlier: 3.609A pdb=" N ILE v 77 " --> pdb=" O TYR v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 85 through 94 Processing helix chain 'v' and resid 103 through 109 Processing helix chain 'v' and resid 158 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 218 through 221 Processing helix chain 'v' and resid 225 through 233 Processing helix chain 'v' and resid 244 through 249 Processing helix chain 'v' and resid 271 through 284 Processing helix chain 'v' and resid 345 through 347 No H-bonds generated for 'chain 'v' and resid 345 through 347' Processing helix chain 'v' and resid 348 through 353 Processing helix chain 'v' and resid 368 through 380 Processing helix chain 'x' and resid 136 through 145 Processing helix chain 'x' and resid 153 through 157 removed outlier: 4.066A pdb=" N LEU x 156 " --> pdb=" O ASN x 153 " (cutoff:3.500A) Processing helix chain 'x' and resid 164 through 175 Processing helix chain 'x' and resid 224 through 230 Processing helix chain 'x' and resid 275 through 280 removed outlier: 3.546A pdb=" N TYR x 278 " --> pdb=" O LYS x 275 " (cutoff:3.500A) Processing helix chain 'x' and resid 290 through 295 removed outlier: 3.646A pdb=" N GLN x 293 " --> pdb=" O LYS x 290 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS x 295 " --> pdb=" O TRP x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 301 through 309 Processing helix chain 'x' and resid 322 through 327 Processing helix chain 'x' and resid 341 through 361 removed outlier: 4.391A pdb=" N GLN x 345 " --> pdb=" O PHE x 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.840A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.553A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 21 removed outlier: 3.508A pdb=" N ALA c 21 " --> pdb=" O ARG c 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 17 through 21' Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.854A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.413A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.535A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 57 Processing helix chain 'e' and resid 63 through 76 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.639A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 46 through 73 removed outlier: 3.624A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing helix chain 'j' and resid 477 through 511 removed outlier: 3.927A pdb=" N THR j 481 " --> pdb=" O LEU j 477 " (cutoff:3.500A) Processing helix chain 'j' and resid 512 through 518 Processing helix chain 'j' and resid 534 through 538 Processing helix chain 'j' and resid 624 through 654 removed outlier: 4.347A pdb=" N ASP j 654 " --> pdb=" O LYS j 650 " (cutoff:3.500A) Processing helix chain 'j' and resid 774 through 806 Processing helix chain 'j' and resid 816 through 820 Processing helix chain 'j' and resid 893 through 904 Processing helix chain 'j' and resid 916 through 927 removed outlier: 3.861A pdb=" N LYS j 922 " --> pdb=" O GLY j 918 " (cutoff:3.500A) Processing helix chain 'j' and resid 927 through 935 removed outlier: 3.548A pdb=" N GLY j 935 " --> pdb=" O PHE j 931 " (cutoff:3.500A) Processing helix chain 'j' and resid 936 through 941 removed outlier: 4.105A pdb=" N PHE j 939 " --> pdb=" O GLY j 936 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 97 removed outlier: 4.394A pdb=" N GLN k 87 " --> pdb=" O GLN k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 202 through 214 Processing helix chain 'k' and resid 313 through 321 Processing helix chain 'k' and resid 334 through 347 Processing helix chain 'k' and resid 435 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.780A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.613A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.694A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.968A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.330A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.953A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.739A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 3.969A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 4.332A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS I 42 " --> pdb=" O TYR A1156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.938A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.950A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 removed outlier: 3.966A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 644 through 645 current: chain 'B' and resid 740 through 741 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.658A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 853 through 862 current: chain 'B' and resid 947 through 956 removed outlier: 8.660A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 962 through 972 current: chain 'L' and resid 39 through 42 Processing sheet with id=AC8, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AC9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.003A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.426A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.538A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD5, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.587A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.730A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG C 156 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 50 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL C 48 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS C 160 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASP C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY C 162 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.672A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.474A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 5 through 6 current: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.469A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.520A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.118A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.590A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.737A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 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 16 through 21 removed outlier: 3.902A pdb=" N VAL M 34 " --> pdb=" O THR M 21 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF3, first strand: chain 'V' and resid 81 through 86 removed outlier: 6.966A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'W' and resid 349 through 354 removed outlier: 4.661A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 522 through 526 removed outlier: 7.777A pdb=" N ILE W 506 " --> pdb=" O VAL W 501 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL W 501 " --> pdb=" O ILE W 506 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER W 508 " --> pdb=" O SER W 499 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 572 through 576 removed outlier: 6.042A pdb=" N ILE W 565 " --> pdb=" O ILE W 554 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE W 554 " --> pdb=" O ILE W 565 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 601 through 603 removed outlier: 6.870A pdb=" N ASP W 621 " --> pdb=" O ILE W 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 650 through 651 removed outlier: 3.559A pdb=" N ALA W 650 " --> pdb=" O VAL W 658 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 697 through 701 removed outlier: 6.906A pdb=" N PHE W 683 " --> pdb=" O VAL W 679 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL W 679 " --> pdb=" O PHE W 683 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE W 685 " --> pdb=" O LEU W 677 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 787 through 791 removed outlier: 4.574A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 396 through 397 Processing sheet with id=AG4, first strand: chain 'm' and resid 644 through 645 Processing sheet with id=AG5, first strand: chain 'm' and resid 790 through 796 removed outlier: 3.833A pdb=" N SER m 792 " --> pdb=" O PHE m 783 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU m 766 " --> pdb=" O GLY m 824 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'm' and resid 959 through 960 removed outlier: 6.875A pdb=" N VAL m 959 " --> pdb=" O TYR m1024 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'm' and resid 1167 through 1175 removed outlier: 6.712A pdb=" N SER m1181 " --> pdb=" O ARG m1173 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL m1175 " --> pdb=" O TYR m1179 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR m1179 " --> pdb=" O VAL m1175 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS m1230 " --> pdb=" O ALA m1189 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLN m1193 " --> pdb=" O LEU m1232 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER m1233 " --> pdb=" O ILE m1220 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE m1220 " --> pdb=" O SER m1233 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 1306 through 1310 removed outlier: 6.747A pdb=" N LEU m1328 " --> pdb=" O VAL m1324 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 1407 through 1412 Processing sheet with id=AH1, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AH2, first strand: chain 'r' and resid 228 through 232 removed outlier: 4.021A pdb=" N LEU r 229 " --> pdb=" O VAL r 246 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL r 246 " --> pdb=" O LEU r 229 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL r 248 " --> pdb=" O ALA r 275 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA r 275 " --> pdb=" O VAL r 248 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'r' and resid 259 through 260 Processing sheet with id=AH4, first strand: chain 'u' and resid 87 through 91 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 87 through 91 current: chain 'u' and resid 178 through 182 removed outlier: 4.923A pdb=" N TYR u 178 " --> pdb=" O MET u 189 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 185 through 193 current: chain 'u' and resid 208 through 223 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 208 through 223 current: chain 'v' and resid 263 through 268 removed outlier: 6.450A pdb=" N ILE v 264 " --> pdb=" O ASP v 302 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP v 302 " --> pdb=" O ILE v 264 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU v 266 " --> pdb=" O ILE v 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 295 through 309 current: chain 'v' and resid 327 through 333 Processing sheet with id=AH5, first strand: chain 'u' and resid 116 through 120 removed outlier: 4.465A pdb=" N TRP u 152 " --> pdb=" O ASN u 117 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU u 119 " --> pdb=" O TRP u 152 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR u 154 " --> pdb=" O GLU u 119 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'v' and resid 29 through 30 Processing sheet with id=AH7, first strand: chain 'x' and resid 247 through 252 removed outlier: 5.935A pdb=" N ILE x 210 " --> pdb=" O VAL x 266 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE x 209 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE x 285 " --> pdb=" O ILE x 209 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL x 211 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE x 312 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE x 285 " --> pdb=" O PHE x 312 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE x 314 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY x 311 " --> pdb=" O LYS x 331 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU x 333 " --> pdb=" O GLY x 311 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR x 313 " --> pdb=" O LEU x 333 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE x 335 " --> pdb=" O TYR x 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS x 315 " --> pdb=" O ILE x 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.931A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AI1, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.626A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AI3, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.018A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.593A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AI6, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.383A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AI8, first strand: chain 'j' and resid 548 through 550 Processing sheet with id=AI9, first strand: chain 'j' and resid 572 through 580 removed outlier: 5.600A pdb=" N ARG j 616 " --> pdb=" O PHE j 590 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU k 122 " --> pdb=" O GLU k 133 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU k 133 " --> pdb=" O LEU k 122 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE k 124 " --> pdb=" O ALA k 131 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 129 through 135 current: chain 'k' and resid 149 through 154 removed outlier: 5.885A pdb=" N VAL k 172 " --> pdb=" O LEU k 154 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'j' and resid 707 through 711 removed outlier: 6.518A pdb=" N LEU j 689 " --> pdb=" O GLU j 672 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU j 672 " --> pdb=" O LEU j 689 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE j 691 " --> pdb=" O LYS j 670 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS j 670 " --> pdb=" O ILE j 691 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N ASN j 673 " --> pdb=" O GLU j 754 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU j 754 " --> pdb=" O ASN j 673 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N LYS j 745 " --> pdb=" O THR j 737 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N THR j 737 " --> pdb=" O LYS j 745 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE j 747 " --> pdb=" O LEU j 735 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE j 730 " --> pdb=" O PHE j 720 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE j 720 " --> pdb=" O ILE j 730 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS j 732 " --> pdb=" O LEU j 718 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU j 718 " --> pdb=" O HIS j 732 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS j 734 " --> pdb=" O LYS j 716 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'j' and resid 821 through 823 Processing sheet with id=AJ3, first strand: chain 'j' and resid 884 through 890 removed outlier: 5.884A pdb=" N PHE j 870 " --> pdb=" O THR j 888 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP j 871 " --> pdb=" O LEU j 860 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU j 860 " --> pdb=" O ASP j 871 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL j 873 " --> pdb=" O ALA j 858 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA j 858 " --> pdb=" O VAL j 873 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL j 875 " --> pdb=" O GLU j 856 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'k' and resid 44 through 47 removed outlier: 5.380A pdb=" N GLY k 18 " --> pdb=" O THR k 8 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL k 4 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N THR k 8 " --> pdb=" O PHE k 80 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N PHE k 80 " --> pdb=" O THR k 8 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TRP k 63 " --> pdb=" O GLY k 79 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'k' and resid 255 through 258 removed outlier: 6.100A pdb=" N GLY k 235 " --> pdb=" O LEU k 229 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU k 229 " --> pdb=" O GLY k 235 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE k 237 " --> pdb=" O ASP k 227 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP k 227 " --> pdb=" O PHE k 237 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL k 223 " --> pdb=" O MET k 241 " (cutoff:3.500A) removed outlier: 13.056A pdb=" N ASP k 227 " --> pdb=" O ASP k 301 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ASP k 301 " --> pdb=" O ASP k 227 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU k 229 " --> pdb=" O GLN k 299 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL k 297 " --> pdb=" O LEU k 231 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N ARG k 292 " --> pdb=" O PRO k 284 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG k 264 " --> pdb=" O GLN k 281 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP k 283 " --> pdb=" O VAL k 262 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL k 262 " --> pdb=" O ASP k 283 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ILE k 351 " --> pdb=" O LEU k 263 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE k 265 " --> pdb=" O ILE k 351 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'k' and resid 305 through 309 removed outlier: 5.418A pdb=" N LEU k 306 " --> pdb=" O THR k 331 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR k 331 " --> pdb=" O LEU k 306 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'k' and resid 391 through 394 removed outlier: 8.440A pdb=" N ASN k 366 " --> pdb=" O ILE k 431 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE k 431 " --> pdb=" O ASN k 366 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN k 430 " --> pdb=" O PHE k 415 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE k 415 " --> pdb=" O ASN k 430 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS k 451 " --> pdb=" O ILE k 399 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL k 401 " --> pdb=" O LYS k 451 " (cutoff:3.500A) 3747 hydrogen bonds defined for protein. 10656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 277 hydrogen bonds 534 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 49.96 Time building geometry restraints manager: 29.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 20919 1.33 - 1.45: 17365 1.45 - 1.58: 44382 1.58 - 1.70: 505 1.70 - 1.82: 517 Bond restraints: 83688 Sorted by residual: bond pdb=" C1' DA T 72 " pdb=" N9 DA T 72 " ideal model delta sigma weight residual 1.460 1.378 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1' DG N -79 " pdb=" N9 DG N -79 " ideal model delta sigma weight residual 1.460 1.378 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C1' DG N -8 " pdb=" N9 DG N -8 " ideal model delta sigma weight residual 1.460 1.378 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1' DA T 61 " pdb=" N9 DA T 61 " ideal model delta sigma weight residual 1.460 1.380 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1' DG N -10 " pdb=" N9 DG N -10 " ideal model delta sigma weight residual 1.460 1.381 0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 83683 not shown) Histogram of bond angle deviations from ideal: 96.31 - 104.09: 1682 104.09 - 111.86: 40766 111.86 - 119.63: 31530 119.63 - 127.40: 38943 127.40 - 135.17: 1127 Bond angle restraints: 114048 Sorted by residual: angle pdb=" O3' DG N -81 " pdb=" C3' DG N -81 " pdb=" C2' DG N -81 " ideal model delta sigma weight residual 111.50 101.15 10.35 1.50e+00 4.44e-01 4.76e+01 angle pdb=" N VAL A1001 " pdb=" CA VAL A1001 " pdb=" C VAL A1001 " ideal model delta sigma weight residual 112.96 107.29 5.67 1.00e+00 1.00e+00 3.21e+01 angle pdb=" O3' U P 10 " pdb=" P U P 11 " pdb=" OP1 U P 11 " ideal model delta sigma weight residual 108.00 124.55 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" O3' DG N -92 " pdb=" C3' DG N -92 " pdb=" C2' DG N -92 " ideal model delta sigma weight residual 111.50 104.27 7.23 1.50e+00 4.44e-01 2.32e+01 angle pdb=" N LEU k 231 " pdb=" CA LEU k 231 " pdb=" C LEU k 231 " ideal model delta sigma weight residual 114.04 108.10 5.94 1.24e+00 6.50e-01 2.30e+01 ... (remaining 114043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.29: 48311 30.29 - 60.58: 2205 60.58 - 90.87: 125 90.87 - 121.16: 1 121.16 - 151.46: 2 Dihedral angle restraints: 50644 sinusoidal: 22819 harmonic: 27825 Sorted by residual: dihedral pdb=" CA TYR A 466 " pdb=" C TYR A 466 " pdb=" N SER A 467 " pdb=" CA SER A 467 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" O4' U P -5 " pdb=" C1' U P -5 " pdb=" N1 U P -5 " pdb=" C2 U P -5 " ideal model delta sinusoidal sigma weight residual -128.00 -58.55 -69.45 1 1.70e+01 3.46e-03 2.16e+01 dihedral pdb=" O4' U P -7 " pdb=" C1' U P -7 " pdb=" N1 U P -7 " pdb=" C2 U P -7 " ideal model delta sinusoidal sigma weight residual -128.00 -62.37 -65.63 1 1.70e+01 3.46e-03 1.95e+01 ... (remaining 50641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 12020 0.102 - 0.204: 653 0.204 - 0.307: 22 0.307 - 0.409: 3 0.409 - 0.511: 1 Chirality restraints: 12699 Sorted by residual: chirality pdb=" P U P 11 " pdb=" OP1 U P 11 " pdb=" OP2 U P 11 " pdb=" O5' U P 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" P DG N-115 " pdb=" OP1 DG N-115 " pdb=" OP2 DG N-115 " pdb=" O5' DG N-115 " both_signs ideal model delta sigma weight residual True 2.35 2.71 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASP k 72 " pdb=" N ASP k 72 " pdb=" C ASP k 72 " pdb=" CB ASP k 72 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 12696 not shown) Planarity restraints: 13884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT T 112 " 0.181 2.00e-02 2.50e+03 1.11e-01 3.09e+02 pdb=" N1 DT T 112 " 0.035 2.00e-02 2.50e+03 pdb=" C2 DT T 112 " -0.042 2.00e-02 2.50e+03 pdb=" O2 DT T 112 " -0.199 2.00e-02 2.50e+03 pdb=" N3 DT T 112 " 0.032 2.00e-02 2.50e+03 pdb=" C4 DT T 112 " 0.059 2.00e-02 2.50e+03 pdb=" O4 DT T 112 " 0.144 2.00e-02 2.50e+03 pdb=" C5 DT T 112 " -0.032 2.00e-02 2.50e+03 pdb=" C7 DT T 112 " -0.144 2.00e-02 2.50e+03 pdb=" C6 DT T 112 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N-102 " 0.183 2.00e-02 2.50e+03 1.04e-01 2.69e+02 pdb=" N1 DT N-102 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT N-102 " -0.050 2.00e-02 2.50e+03 pdb=" O2 DT N-102 " -0.150 2.00e-02 2.50e+03 pdb=" N3 DT N-102 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DT N-102 " 0.040 2.00e-02 2.50e+03 pdb=" O4 DT N-102 " 0.171 2.00e-02 2.50e+03 pdb=" C5 DT N-102 " -0.045 2.00e-02 2.50e+03 pdb=" C7 DT N-102 " -0.118 2.00e-02 2.50e+03 pdb=" C6 DT N-102 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG N-111 " 0.181 2.00e-02 2.50e+03 7.52e-02 1.70e+02 pdb=" N9 DG N-111 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DG N-111 " -0.073 2.00e-02 2.50e+03 pdb=" N7 DG N-111 " -0.067 2.00e-02 2.50e+03 pdb=" C5 DG N-111 " -0.034 2.00e-02 2.50e+03 pdb=" C6 DG N-111 " 0.031 2.00e-02 2.50e+03 pdb=" O6 DG N-111 " 0.103 2.00e-02 2.50e+03 pdb=" N1 DG N-111 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DG N-111 " 0.015 2.00e-02 2.50e+03 pdb=" N2 DG N-111 " -0.067 2.00e-02 2.50e+03 pdb=" N3 DG N-111 " -0.048 2.00e-02 2.50e+03 pdb=" C4 DG N-111 " -0.053 2.00e-02 2.50e+03 ... (remaining 13881 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 12 2.20 - 2.88: 28730 2.88 - 3.55: 114823 3.55 - 4.23: 191581 4.23 - 4.90: 328861 Nonbonded interactions: 664007 Sorted by model distance: nonbonded pdb=" O THR k 145 " pdb=" CD1 TYR k 253 " model vdw 1.525 3.340 nonbonded pdb=" O THR k 145 " pdb=" CE1 TYR k 253 " model vdw 1.796 3.340 nonbonded pdb=" OP1 U P 11 " pdb="MG MG A1803 " model vdw 1.958 2.170 nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR K 57 " pdb=" OE1 GLN K 76 " model vdw 2.167 2.440 ... (remaining 664002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.090 Extract box with map and model: 6.990 Check model and map are aligned: 0.950 Set scattering table: 0.610 Process input model: 217.830 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 232.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.006 0.088 83688 Z= 0.386 Angle : 0.744 16.546 114048 Z= 0.467 Chirality : 0.049 0.511 12699 Planarity : 0.007 0.247 13884 Dihedral : 15.601 151.456 32610 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.09), residues: 9398 helix: 1.89 (0.08), residues: 4097 sheet: 0.35 (0.14), residues: 1382 loop : -0.01 (0.10), residues: 3919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.004 TRP k 56 HIS 0.027 0.001 HIS j 692 PHE 0.069 0.003 PHE k 300 TYR 0.081 0.002 TYR k 60 ARG 0.022 0.001 ARG j 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2943 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2943 time to evaluate : 6.966 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: A 16 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8183 (mt-10) REVERT: A 37 TYR cc_start: 0.8540 (m-80) cc_final: 0.8337 (m-10) REVERT: A 54 ASN cc_start: 0.9064 (m110) cc_final: 0.8726 (m110) REVERT: A 65 PHE cc_start: 0.8513 (m-10) cc_final: 0.8113 (m-10) REVERT: A 72 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8004 (mp0) REVERT: A 84 MET cc_start: 0.8365 (ttm) cc_final: 0.8155 (ttm) REVERT: A 116 ASP cc_start: 0.7947 (m-30) cc_final: 0.7699 (p0) REVERT: A 203 LEU cc_start: 0.9366 (mt) cc_final: 0.9097 (mm) REVERT: A 242 VAL cc_start: 0.9532 (t) cc_final: 0.9253 (p) REVERT: A 282 MET cc_start: 0.8144 (ptp) cc_final: 0.7848 (ptp) REVERT: A 290 ILE cc_start: 0.9462 (mt) cc_final: 0.9017 (mm) REVERT: A 306 ASP cc_start: 0.8666 (t0) cc_final: 0.8074 (t0) REVERT: A 349 SER cc_start: 0.9725 (p) cc_final: 0.9509 (p) REVERT: A 415 ASP cc_start: 0.9019 (t0) cc_final: 0.8409 (t70) REVERT: A 448 GLN cc_start: 0.8573 (mp10) cc_final: 0.8112 (mt0) REVERT: A 454 MET cc_start: 0.8450 (mpp) cc_final: 0.7961 (mpp) REVERT: A 477 SER cc_start: 0.9694 (m) cc_final: 0.9421 (p) REVERT: A 480 ASN cc_start: 0.8750 (t0) cc_final: 0.8518 (t0) REVERT: A 497 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 526 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8452 (mm-40) REVERT: A 533 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8734 (tmt170) REVERT: A 535 MET cc_start: 0.9080 (ttt) cc_final: 0.8677 (ttp) REVERT: A 540 THR cc_start: 0.9412 (m) cc_final: 0.9207 (p) REVERT: A 544 TYR cc_start: 0.8978 (t80) cc_final: 0.8685 (t80) REVERT: A 548 MET cc_start: 0.8516 (mtm) cc_final: 0.7842 (mtm) REVERT: A 551 LEU cc_start: 0.9276 (mt) cc_final: 0.9031 (mt) REVERT: A 617 VAL cc_start: 0.9577 (t) cc_final: 0.9370 (p) REVERT: A 630 LEU cc_start: 0.9639 (tp) cc_final: 0.9392 (tp) REVERT: A 706 LYS cc_start: 0.7937 (tmtt) cc_final: 0.7651 (tptt) REVERT: A 719 VAL cc_start: 0.9726 (t) cc_final: 0.9477 (m) REVERT: A 728 ASP cc_start: 0.8569 (m-30) cc_final: 0.8367 (m-30) REVERT: A 735 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 757 ILE cc_start: 0.9398 (tp) cc_final: 0.8944 (tp) REVERT: A 797 SER cc_start: 0.9172 (t) cc_final: 0.8741 (p) REVERT: A 813 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8191 (mt-10) REVERT: A 848 ASP cc_start: 0.8097 (p0) cc_final: 0.7793 (p0) REVERT: A 857 THR cc_start: 0.9667 (m) cc_final: 0.9461 (p) REVERT: A 863 ASP cc_start: 0.8797 (m-30) cc_final: 0.8499 (m-30) REVERT: A 885 ASP cc_start: 0.7826 (m-30) cc_final: 0.7514 (m-30) REVERT: A 929 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8570 (mm-30) REVERT: A 971 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 1035 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 1073 SER cc_start: 0.9522 (m) cc_final: 0.8941 (p) REVERT: A 1079 THR cc_start: 0.9272 (m) cc_final: 0.8985 (p) REVERT: A 1098 LEU cc_start: 0.8637 (mt) cc_final: 0.8223 (mt) REVERT: A 1113 ILE cc_start: 0.9332 (pt) cc_final: 0.9074 (pt) REVERT: A 1207 LYS cc_start: 0.9390 (mmtt) cc_final: 0.9092 (mmtm) REVERT: A 1217 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9233 (mmmm) REVERT: A 1222 PHE cc_start: 0.7691 (m-10) cc_final: 0.6267 (m-80) REVERT: A 1242 CYS cc_start: 0.8866 (t) cc_final: 0.8416 (p) REVERT: A 1244 VAL cc_start: 0.7515 (t) cc_final: 0.7046 (t) REVERT: A 1267 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 1271 LEU cc_start: 0.9032 (mt) cc_final: 0.8786 (mt) REVERT: A 1283 SER cc_start: 0.9096 (p) cc_final: 0.8503 (m) REVERT: A 1284 LYS cc_start: 0.8416 (tptt) cc_final: 0.8153 (mmmm) REVERT: A 1345 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8307 (mm-30) REVERT: A 1403 CYS cc_start: 0.9231 (p) cc_final: 0.8846 (p) REVERT: A 1406 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 1435 GLN cc_start: 0.7966 (mt0) cc_final: 0.7757 (mt0) REVERT: A 1436 LEU cc_start: 0.9320 (tp) cc_final: 0.8907 (mt) REVERT: A 1447 MET cc_start: 0.8929 (mmm) cc_final: 0.8346 (mmm) REVERT: B 14 THR cc_start: 0.9459 (m) cc_final: 0.9107 (p) REVERT: B 39 ASP cc_start: 0.8290 (m-30) cc_final: 0.7905 (m-30) REVERT: B 53 GLU cc_start: 0.8752 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 57 ILE cc_start: 0.9115 (mt) cc_final: 0.8509 (tp) REVERT: B 118 ASP cc_start: 0.8767 (m-30) cc_final: 0.8164 (m-30) REVERT: B 119 MET cc_start: 0.8487 (mtt) cc_final: 0.8239 (mtt) REVERT: B 120 GLU cc_start: 0.8362 (tp30) cc_final: 0.8026 (tp30) REVERT: B 182 LYS cc_start: 0.9278 (mttt) cc_final: 0.8984 (mtmm) REVERT: B 199 SER cc_start: 0.9409 (t) cc_final: 0.8879 (p) REVERT: B 214 VAL cc_start: 0.9489 (t) cc_final: 0.9187 (m) REVERT: B 233 SER cc_start: 0.9262 (m) cc_final: 0.8998 (t) REVERT: B 269 LYS cc_start: 0.9029 (mttm) cc_final: 0.8573 (mtpt) REVERT: B 288 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8495 (mt-10) REVERT: B 290 LEU cc_start: 0.9646 (mm) cc_final: 0.9430 (mm) REVERT: B 320 GLU cc_start: 0.8862 (mp0) cc_final: 0.8207 (mp0) REVERT: B 373 TYR cc_start: 0.9395 (t80) cc_final: 0.9157 (t80) REVERT: B 384 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 418 THR cc_start: 0.9754 (m) cc_final: 0.9455 (p) REVERT: B 437 LEU cc_start: 0.8959 (tp) cc_final: 0.8616 (tp) REVERT: B 463 LYS cc_start: 0.8201 (pptt) cc_final: 0.7788 (pttp) REVERT: B 507 LEU cc_start: 0.9563 (tp) cc_final: 0.9328 (tp) REVERT: B 549 ASN cc_start: 0.9410 (m-40) cc_final: 0.8088 (m110) REVERT: B 550 PHE cc_start: 0.8950 (m-80) cc_final: 0.8681 (m-80) REVERT: B 595 ASP cc_start: 0.8404 (m-30) cc_final: 0.7859 (m-30) REVERT: B 611 ASP cc_start: 0.8071 (t0) cc_final: 0.7672 (t0) REVERT: B 621 THR cc_start: 0.9382 (p) cc_final: 0.9000 (t) REVERT: B 681 LEU cc_start: 0.9444 (mt) cc_final: 0.9191 (mt) REVERT: B 747 MET cc_start: 0.8962 (mmm) cc_final: 0.8634 (mmp) REVERT: B 754 SER cc_start: 0.9632 (m) cc_final: 0.9372 (m) REVERT: B 785 TYR cc_start: 0.9352 (p90) cc_final: 0.8874 (p90) REVERT: B 789 MET cc_start: 0.9001 (mmt) cc_final: 0.8355 (mmm) REVERT: B 836 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7857 (mm-30) REVERT: B 846 ILE cc_start: 0.9342 (mt) cc_final: 0.9020 (mt) REVERT: B 847 ASP cc_start: 0.8901 (m-30) cc_final: 0.8355 (m-30) REVERT: B 866 PHE cc_start: 0.8300 (m-80) cc_final: 0.7904 (m-80) REVERT: B 923 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 939 THR cc_start: 0.9414 (m) cc_final: 0.9126 (p) REVERT: B 961 LEU cc_start: 0.9397 (mm) cc_final: 0.9143 (mp) REVERT: B 996 HIS cc_start: 0.9286 (t-90) cc_final: 0.8655 (t70) REVERT: B 1149 GLU cc_start: 0.7510 (tt0) cc_final: 0.7283 (tt0) REVERT: B 1165 ILE cc_start: 0.9613 (mt) cc_final: 0.9410 (mm) REVERT: B 1202 LEU cc_start: 0.9537 (tp) cc_final: 0.9230 (tp) REVERT: C 13 GLN cc_start: 0.7506 (mt0) cc_final: 0.6770 (mt0) REVERT: C 48 VAL cc_start: 0.9440 (t) cc_final: 0.9061 (p) REVERT: C 100 LEU cc_start: 0.9358 (tt) cc_final: 0.9062 (tt) REVERT: C 112 ASP cc_start: 0.8161 (m-30) cc_final: 0.7003 (m-30) REVERT: C 138 TYR cc_start: 0.7089 (m-80) cc_final: 0.6603 (m-80) REVERT: C 186 LEU cc_start: 0.9564 (mt) cc_final: 0.9147 (mp) REVERT: C 261 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8342 (tp30) REVERT: D 33 GLU cc_start: 0.9038 (pm20) cc_final: 0.8543 (pm20) REVERT: D 53 LEU cc_start: 0.8344 (mp) cc_final: 0.7891 (mp) REVERT: D 69 ARG cc_start: 0.9285 (ttp-110) cc_final: 0.9002 (mmp80) REVERT: D 86 ASP cc_start: 0.7323 (m-30) cc_final: 0.7011 (m-30) REVERT: D 138 HIS cc_start: 0.8302 (t-90) cc_final: 0.7820 (t70) REVERT: D 144 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8830 (tp-100) REVERT: D 160 ILE cc_start: 0.7252 (mt) cc_final: 0.7050 (mt) REVERT: D 183 ASP cc_start: 0.6947 (m-30) cc_final: 0.6617 (t0) REVERT: E 14 SER cc_start: 0.9767 (m) cc_final: 0.9487 (p) REVERT: E 24 ASP cc_start: 0.8382 (m-30) cc_final: 0.8124 (m-30) REVERT: E 34 MET cc_start: 0.9172 (tpp) cc_final: 0.8794 (tpp) REVERT: E 73 ASP cc_start: 0.8938 (p0) cc_final: 0.8592 (p0) REVERT: E 92 MET cc_start: 0.9168 (tpp) cc_final: 0.8894 (tpt) REVERT: E 132 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8003 (mt-10) REVERT: E 133 THR cc_start: 0.9615 (p) cc_final: 0.9366 (t) REVERT: E 135 GLN cc_start: 0.8888 (tt0) cc_final: 0.8414 (tp-100) REVERT: E 189 LEU cc_start: 0.9213 (mt) cc_final: 0.8986 (mt) REVERT: E 193 GLN cc_start: 0.9168 (mt0) cc_final: 0.8787 (mt0) REVERT: E 202 GLU cc_start: 0.7788 (pt0) cc_final: 0.7559 (pt0) REVERT: F 140 ASP cc_start: 0.8674 (p0) cc_final: 0.8466 (p0) REVERT: F 154 ASP cc_start: 0.8348 (m-30) cc_final: 0.8007 (m-30) REVERT: G 2 PHE cc_start: 0.8693 (m-80) cc_final: 0.8386 (m-80) REVERT: G 34 VAL cc_start: 0.9100 (t) cc_final: 0.8834 (p) REVERT: G 65 SER cc_start: 0.9062 (p) cc_final: 0.8753 (p) REVERT: G 73 LYS cc_start: 0.9377 (mttt) cc_final: 0.8668 (mtpp) REVERT: G 99 PHE cc_start: 0.7205 (p90) cc_final: 0.6849 (p90) REVERT: G 122 ASN cc_start: 0.7910 (t0) cc_final: 0.7536 (t0) REVERT: G 158 TYR cc_start: 0.8724 (m-80) cc_final: 0.8209 (m-80) REVERT: H 16 ASP cc_start: 0.8102 (t0) cc_final: 0.7888 (t0) REVERT: H 32 THR cc_start: 0.9177 (p) cc_final: 0.8938 (t) REVERT: H 54 SER cc_start: 0.9303 (m) cc_final: 0.9100 (t) REVERT: H 133 SER cc_start: 0.8893 (p) cc_final: 0.8541 (t) REVERT: I 13 MET cc_start: 0.8512 (ttm) cc_final: 0.8129 (tpp) REVERT: I 25 LEU cc_start: 0.6559 (tp) cc_final: 0.6332 (tp) REVERT: I 28 SER cc_start: 0.8329 (t) cc_final: 0.8020 (p) REVERT: I 44 TYR cc_start: 0.8374 (t80) cc_final: 0.8007 (t80) REVERT: I 85 PHE cc_start: 0.8785 (p90) cc_final: 0.8447 (p90) REVERT: K 38 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7892 (mm-30) REVERT: L 30 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8372 (mttt) REVERT: L 67 ILE cc_start: 0.8980 (mt) cc_final: 0.8422 (tp) REVERT: M 68 ASP cc_start: 0.8306 (m-30) cc_final: 0.6900 (m-30) REVERT: V 39 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7975 (ptp-170) REVERT: V 65 HIS cc_start: 0.6739 (m90) cc_final: 0.5572 (t70) REVERT: V 82 TYR cc_start: 0.7199 (m-80) cc_final: 0.6426 (m-80) REVERT: W 226 ILE cc_start: 0.8692 (mt) cc_final: 0.8452 (mt) REVERT: W 227 TRP cc_start: 0.7572 (m-90) cc_final: 0.6142 (m-90) REVERT: W 236 GLU cc_start: 0.7306 (mp0) cc_final: 0.5154 (mm-30) REVERT: W 268 PHE cc_start: 0.8810 (m-10) cc_final: 0.8586 (m-80) REVERT: W 272 VAL cc_start: 0.9279 (t) cc_final: 0.8344 (t) REVERT: W 300 LEU cc_start: 0.9208 (mt) cc_final: 0.8971 (mp) REVERT: W 304 VAL cc_start: 0.8767 (p) cc_final: 0.8409 (m) REVERT: W 444 LEU cc_start: 0.8608 (mt) cc_final: 0.8383 (pt) REVERT: W 478 PHE cc_start: 0.6691 (m-80) cc_final: 0.6331 (m-80) REVERT: W 484 VAL cc_start: 0.9070 (m) cc_final: 0.8345 (p) REVERT: W 495 THR cc_start: 0.8499 (p) cc_final: 0.7900 (t) REVERT: W 521 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7275 (mm-30) REVERT: W 523 VAL cc_start: 0.8564 (t) cc_final: 0.8026 (m) REVERT: W 585 ASP cc_start: 0.7510 (t0) cc_final: 0.7120 (t0) REVERT: W 618 ASP cc_start: 0.5968 (m-30) cc_final: 0.5674 (m-30) REVERT: W 648 GLN cc_start: 0.9160 (tt0) cc_final: 0.8258 (tm-30) REVERT: W 663 THR cc_start: 0.8448 (m) cc_final: 0.8211 (t) REVERT: W 678 HIS cc_start: 0.9411 (m90) cc_final: 0.8977 (m90) REVERT: W 679 VAL cc_start: 0.8777 (t) cc_final: 0.7317 (t) REVERT: W 760 GLN cc_start: 0.7078 (mt0) cc_final: 0.6801 (mm110) REVERT: W 777 ARG cc_start: 0.6753 (mmm160) cc_final: 0.6352 (ptp90) REVERT: W 795 PHE cc_start: 0.8304 (m-80) cc_final: 0.7709 (m-80) REVERT: W 796 LEU cc_start: 0.8711 (mt) cc_final: 0.8453 (mm) REVERT: W 804 TRP cc_start: 0.6536 (m100) cc_final: 0.6018 (m100) REVERT: m 240 ILE cc_start: 0.4234 (mt) cc_final: 0.3902 (pt) REVERT: m 241 PHE cc_start: 0.7209 (m-80) cc_final: 0.6767 (m-10) REVERT: m 288 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6896 (tm-30) REVERT: m 310 PHE cc_start: 0.8731 (m-80) cc_final: 0.8343 (m-10) REVERT: m 338 LEU cc_start: 0.8356 (mt) cc_final: 0.8060 (mt) REVERT: m 341 GLU cc_start: 0.7336 (tp30) cc_final: 0.7019 (pt0) REVERT: m 386 ASN cc_start: 0.9110 (m-40) cc_final: 0.8814 (m110) REVERT: m 422 LEU cc_start: 0.7332 (mt) cc_final: 0.7021 (mt) REVERT: m 461 SER cc_start: 0.9044 (t) cc_final: 0.8560 (p) REVERT: m 627 LEU cc_start: 0.8073 (tt) cc_final: 0.7807 (mm) REVERT: m 657 LEU cc_start: 0.8997 (mm) cc_final: 0.8705 (mm) REVERT: m 669 ASN cc_start: 0.8919 (m110) cc_final: 0.8528 (m-40) REVERT: m 726 SER cc_start: 0.9307 (t) cc_final: 0.8759 (p) REVERT: m 784 MET cc_start: 0.8403 (ttp) cc_final: 0.7668 (ptp) REVERT: m 789 ASP cc_start: 0.7924 (m-30) cc_final: 0.7153 (p0) REVERT: m 807 ASP cc_start: 0.9501 (t0) cc_final: 0.9105 (m-30) REVERT: m 818 ILE cc_start: 0.7836 (mm) cc_final: 0.6948 (pt) REVERT: m 830 ILE cc_start: 0.9258 (pt) cc_final: 0.9041 (pt) REVERT: m 841 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8639 (tp30) REVERT: m 845 GLU cc_start: 0.8585 (tp30) cc_final: 0.7758 (pt0) REVERT: m 918 TYR cc_start: 0.8164 (m-80) cc_final: 0.7709 (m-80) REVERT: m 922 ASP cc_start: 0.9546 (t0) cc_final: 0.9302 (t0) REVERT: m 946 VAL cc_start: 0.9264 (t) cc_final: 0.9036 (t) REVERT: m 1152 GLN cc_start: 0.9462 (tt0) cc_final: 0.9212 (tp-100) REVERT: m 1166 MET cc_start: 0.8671 (mmm) cc_final: 0.8137 (mtp) REVERT: m 1173 ARG cc_start: 0.6137 (ttt180) cc_final: 0.5056 (ptm160) REVERT: m 1230 CYS cc_start: 0.9194 (p) cc_final: 0.8589 (t) REVERT: n 160 ILE cc_start: 0.7651 (mt) cc_final: 0.7426 (mt) REVERT: n 187 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7607 (mttm) REVERT: n 189 LYS cc_start: 0.8146 (mttt) cc_final: 0.7629 (mmtp) REVERT: n 200 ARG cc_start: 0.6839 (ttt180) cc_final: 0.6092 (mmm-85) REVERT: n 260 MET cc_start: 0.8841 (mmt) cc_final: 0.8355 (mmt) REVERT: q 338 TRP cc_start: 0.6415 (m100) cc_final: 0.6022 (m100) REVERT: q 459 ASN cc_start: 0.7971 (m-40) cc_final: 0.7762 (m110) REVERT: q 644 MET cc_start: -0.0061 (ttm) cc_final: -0.2250 (tmm) REVERT: q 720 PHE cc_start: 0.9171 (m-80) cc_final: 0.8940 (m-80) REVERT: q 721 MET cc_start: 0.8183 (mmm) cc_final: 0.7947 (mmm) REVERT: q 741 SER cc_start: 0.4936 (m) cc_final: 0.4730 (p) REVERT: q 763 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9197 (mm-30) REVERT: q 773 LEU cc_start: 0.8168 (tp) cc_final: 0.7812 (tp) REVERT: q 775 VAL cc_start: 0.7350 (t) cc_final: 0.6971 (p) REVERT: q 777 GLU cc_start: 0.8741 (tp30) cc_final: 0.8085 (mm-30) REVERT: q 911 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6649 (mm-30) REVERT: r 329 MET cc_start: -0.3142 (tmm) cc_final: -0.3926 (ttp) REVERT: r 401 SER cc_start: 0.9021 (m) cc_final: 0.8651 (p) REVERT: u 122 ASP cc_start: 0.6138 (t0) cc_final: 0.5936 (t70) REVERT: u 148 ASN cc_start: 0.7539 (m-40) cc_final: 0.6781 (p0) REVERT: u 149 THR cc_start: 0.6696 (m) cc_final: 0.6340 (t) REVERT: u 171 ILE cc_start: 0.5357 (mm) cc_final: 0.5010 (tp) REVERT: u 177 THR cc_start: 0.6140 (p) cc_final: 0.5625 (p) REVERT: u 202 GLU cc_start: 0.6154 (tt0) cc_final: 0.5890 (tt0) REVERT: u 246 SER cc_start: 0.7603 (p) cc_final: 0.5352 (t) REVERT: u 247 TYR cc_start: 0.8606 (m-80) cc_final: 0.8361 (m-10) REVERT: u 256 ASP cc_start: 0.8192 (t0) cc_final: 0.7603 (t0) REVERT: u 265 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8924 (mm-30) REVERT: u 268 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7214 (mm-30) REVERT: u 272 TYR cc_start: 0.7534 (m-80) cc_final: 0.6921 (m-80) REVERT: v 49 LEU cc_start: 0.8554 (tp) cc_final: 0.8351 (pp) REVERT: v 63 MET cc_start: 0.6105 (mmm) cc_final: 0.4899 (ptm) REVERT: v 169 THR cc_start: 0.8459 (p) cc_final: 0.8218 (p) REVERT: v 180 ASN cc_start: 0.7295 (t0) cc_final: 0.7043 (t0) REVERT: v 262 LYS cc_start: 0.6261 (ptpt) cc_final: 0.6050 (tptt) REVERT: v 294 HIS cc_start: 0.6795 (m-70) cc_final: 0.6523 (m170) REVERT: v 333 ILE cc_start: 0.7254 (mm) cc_final: 0.6999 (tp) REVERT: x 227 GLU cc_start: 0.8769 (mp0) cc_final: 0.8563 (pm20) REVERT: x 230 GLN cc_start: 0.8907 (tt0) cc_final: 0.8193 (tt0) REVERT: x 240 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6397 (mt-10) REVERT: x 265 VAL cc_start: 0.8907 (t) cc_final: 0.8667 (m) REVERT: x 268 ASN cc_start: 0.7379 (t0) cc_final: 0.6905 (p0) REVERT: x 272 LEU cc_start: 0.7488 (mm) cc_final: 0.7237 (mm) REVERT: x 282 VAL cc_start: 0.8659 (t) cc_final: 0.8416 (t) REVERT: x 308 LYS cc_start: 0.8692 (mttm) cc_final: 0.8451 (tttt) REVERT: x 316 TYR cc_start: 0.7863 (m-80) cc_final: 0.7535 (m-10) REVERT: x 329 ASN cc_start: 0.8140 (t0) cc_final: 0.7917 (t0) REVERT: x 339 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7730 (mt-10) REVERT: x 348 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7971 (tt0) REVERT: x 352 ASP cc_start: 0.8325 (m-30) cc_final: 0.7986 (m-30) REVERT: j 652 MET cc_start: -0.3226 (mmt) cc_final: -0.3597 (mtt) REVERT: j 722 PRO cc_start: 0.4861 (Cg_endo) cc_final: 0.4122 (Cg_exo) REVERT: j 788 LYS cc_start: 0.5161 (mttt) cc_final: 0.4764 (ttpt) REVERT: j 793 LYS cc_start: 0.6248 (tttt) cc_final: 0.5940 (mttp) REVERT: j 921 MET cc_start: 0.2962 (mmm) cc_final: 0.2535 (mmm) REVERT: k 21 ARG cc_start: 0.4755 (mtt180) cc_final: 0.4447 (ttp-170) REVERT: k 70 ARG cc_start: 0.1683 (mtt180) cc_final: 0.1307 (tpt170) REVERT: k 86 GLN cc_start: 0.7162 (mt0) cc_final: 0.6546 (pp30) outliers start: 0 outliers final: 0 residues processed: 2943 average time/residue: 0.8115 time to fit residues: 3969.1848 Evaluate side-chains 2017 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2017 time to evaluate : 6.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 811 optimal weight: 50.0000 chunk 728 optimal weight: 9.9990 chunk 404 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 491 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 753 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 458 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 872 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 295 GLN A 340 ASN A 516 GLN A 546 GLN A 563 GLN A 596 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS A 968 ASN A1021 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 843 GLN B 958 GLN B1104 HIS B1211 ASN E 145 HIS E 178 GLN H 44 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 HIS I 87 GLN M 29 ASN ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 264 GLN W 283 ASN W 391 GLN ** W 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 479 GLN W 567 ASN ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 347 GLN m 358 HIS m 425 HIS m 526 GLN ** m 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 840 ASN m 896 ASN m 912 GLN m 970 HIS ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN q 238 HIS ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 250 ASN ** q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 438 ASN ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 409 GLN u 148 ASN ** u 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 158 ASN v 209 GLN ** v 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS ** j 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 589 ASN j 693 GLN ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 864 GLN k 127 ASN k 299 GLN k 359 GLN k 426 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 83688 Z= 0.492 Angle : 0.714 11.546 114048 Z= 0.379 Chirality : 0.045 0.249 12699 Planarity : 0.005 0.069 13884 Dihedral : 15.703 141.432 13291 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.87 % Favored : 97.12 % Rotamer: Outliers : 2.70 % Allowed : 11.39 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.09), residues: 9398 helix: 1.82 (0.08), residues: 4148 sheet: 0.37 (0.14), residues: 1374 loop : -0.01 (0.10), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP m 385 HIS 0.011 0.002 HIS B1015 PHE 0.030 0.002 PHE r 355 TYR 0.033 0.002 TYR j 585 ARG 0.010 0.001 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2185 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1957 time to evaluate : 7.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: A 36 GLU cc_start: 0.8236 (pm20) cc_final: 0.7848 (pm20) REVERT: A 37 TYR cc_start: 0.8793 (m-80) cc_final: 0.8125 (m-10) REVERT: A 54 ASN cc_start: 0.9109 (m110) cc_final: 0.8718 (m110) REVERT: A 65 PHE cc_start: 0.8528 (m-10) cc_final: 0.8249 (m-10) REVERT: A 72 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8216 (mp0) REVERT: A 115 LEU cc_start: 0.8369 (mt) cc_final: 0.7795 (mp) REVERT: A 116 ASP cc_start: 0.8201 (m-30) cc_final: 0.7792 (p0) REVERT: A 272 LYS cc_start: 0.9305 (ttmt) cc_final: 0.9027 (mttt) REVERT: A 306 ASP cc_start: 0.8693 (t0) cc_final: 0.8012 (t0) REVERT: A 349 SER cc_start: 0.9651 (p) cc_final: 0.9270 (p) REVERT: A 379 GLU cc_start: 0.8387 (tt0) cc_final: 0.8173 (mt-10) REVERT: A 409 ASP cc_start: 0.8175 (p0) cc_final: 0.7914 (p0) REVERT: A 417 ARG cc_start: 0.7874 (mtm110) cc_final: 0.7625 (mtm110) REVERT: A 533 ARG cc_start: 0.9314 (ttp80) cc_final: 0.8789 (tmt170) REVERT: A 535 MET cc_start: 0.9153 (ttt) cc_final: 0.8730 (ttp) REVERT: A 540 THR cc_start: 0.9442 (m) cc_final: 0.9192 (p) REVERT: A 606 MET cc_start: 0.8646 (tpp) cc_final: 0.8262 (tpp) REVERT: A 617 VAL cc_start: 0.9496 (t) cc_final: 0.9245 (p) REVERT: A 641 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8192 (ttpt) REVERT: A 712 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8449 (ttm170) REVERT: A 728 ASP cc_start: 0.8730 (m-30) cc_final: 0.8522 (m-30) REVERT: A 769 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8898 (mm-40) REVERT: A 770 MET cc_start: 0.8513 (tpp) cc_final: 0.8248 (tpp) REVERT: A 813 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 847 GLU cc_start: 0.8388 (pt0) cc_final: 0.8131 (pt0) REVERT: A 863 ASP cc_start: 0.8930 (m-30) cc_final: 0.8525 (m-30) REVERT: A 971 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8623 (tm-30) REVERT: A 1035 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 1073 SER cc_start: 0.9458 (m) cc_final: 0.8965 (p) REVERT: A 1098 LEU cc_start: 0.8769 (mt) cc_final: 0.8417 (mt) REVERT: A 1207 LYS cc_start: 0.9424 (mmtt) cc_final: 0.9092 (mmtm) REVERT: A 1211 MET cc_start: 0.8034 (mmm) cc_final: 0.6872 (mmm) REVERT: A 1217 LYS cc_start: 0.9500 (mmtt) cc_final: 0.8997 (mmmm) REVERT: A 1284 LYS cc_start: 0.8691 (tptt) cc_final: 0.8293 (ttmm) REVERT: A 1406 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 1447 MET cc_start: 0.8881 (mmm) cc_final: 0.8334 (mmm) REVERT: A 1453 LEU cc_start: 0.9433 (mt) cc_final: 0.9090 (tp) REVERT: B 14 THR cc_start: 0.9377 (m) cc_final: 0.9128 (p) REVERT: B 35 LEU cc_start: 0.9359 (mt) cc_final: 0.8888 (mm) REVERT: B 39 ASP cc_start: 0.8286 (m-30) cc_final: 0.7993 (m-30) REVERT: B 53 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8641 (tp30) REVERT: B 182 LYS cc_start: 0.9486 (mttt) cc_final: 0.9172 (mtmm) REVERT: B 183 MET cc_start: 0.8966 (mmm) cc_final: 0.8673 (mmm) REVERT: B 199 SER cc_start: 0.9489 (t) cc_final: 0.8737 (p) REVERT: B 231 ILE cc_start: 0.9381 (tt) cc_final: 0.8960 (tp) REVERT: B 233 SER cc_start: 0.9328 (m) cc_final: 0.9033 (t) REVERT: B 269 LYS cc_start: 0.8914 (mttm) cc_final: 0.8633 (mtpt) REVERT: B 270 GLN cc_start: 0.8569 (mm110) cc_final: 0.8265 (mm110) REVERT: B 283 VAL cc_start: 0.9318 (m) cc_final: 0.8871 (p) REVERT: B 339 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8782 (tm-30) REVERT: B 343 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8810 (mm-40) REVERT: B 363 PHE cc_start: 0.8139 (m-80) cc_final: 0.7842 (m-80) REVERT: B 384 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8538 (mp0) REVERT: B 486 SER cc_start: 0.9757 (OUTLIER) cc_final: 0.9500 (p) REVERT: B 492 ASN cc_start: 0.9622 (t0) cc_final: 0.9262 (t0) REVERT: B 548 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9207 (tp) REVERT: B 549 ASN cc_start: 0.8308 (m-40) cc_final: 0.7419 (m-40) REVERT: B 573 ILE cc_start: 0.9590 (mt) cc_final: 0.9384 (mp) REVERT: B 584 ARG cc_start: 0.8299 (ptp-110) cc_final: 0.8075 (mtp85) REVERT: B 589 LEU cc_start: 0.9534 (tp) cc_final: 0.9285 (tp) REVERT: B 595 ASP cc_start: 0.8475 (m-30) cc_final: 0.7952 (m-30) REVERT: B 611 ASP cc_start: 0.8065 (t0) cc_final: 0.7649 (t0) REVERT: B 656 GLN cc_start: 0.8746 (mt0) cc_final: 0.8527 (mt0) REVERT: B 681 LEU cc_start: 0.9534 (mt) cc_final: 0.9277 (mt) REVERT: B 691 ASP cc_start: 0.8940 (p0) cc_final: 0.8561 (p0) REVERT: B 702 MET cc_start: 0.8869 (tpp) cc_final: 0.8568 (tpp) REVERT: B 754 SER cc_start: 0.9593 (m) cc_final: 0.9379 (m) REVERT: B 786 ASN cc_start: 0.8073 (p0) cc_final: 0.7848 (p0) REVERT: B 835 GLN cc_start: 0.8077 (mt0) cc_final: 0.7790 (mt0) REVERT: B 884 ARG cc_start: 0.6871 (mmt-90) cc_final: 0.6637 (mmt-90) REVERT: B 904 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7034 (ttt-90) REVERT: B 924 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8517 (mp0) REVERT: B 931 TYR cc_start: 0.8932 (p90) cc_final: 0.8566 (p90) REVERT: B 1050 LEU cc_start: 0.9311 (tt) cc_final: 0.8984 (tt) REVERT: B 1112 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8370 (mm-40) REVERT: B 1128 LEU cc_start: 0.9358 (mp) cc_final: 0.9001 (mp) REVERT: B 1134 GLU cc_start: 0.9080 (mp0) cc_final: 0.8460 (mp0) REVERT: B 1153 GLU cc_start: 0.8068 (mp0) cc_final: 0.7843 (mp0) REVERT: B 1168 LEU cc_start: 0.9423 (mt) cc_final: 0.9135 (mp) REVERT: B 1203 LEU cc_start: 0.9680 (tp) cc_final: 0.9444 (tt) REVERT: C 210 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8347 (mm-30) REVERT: D 38 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7947 (mp-120) REVERT: D 144 GLN cc_start: 0.9427 (mm-40) cc_final: 0.8921 (tp-100) REVERT: D 183 ASP cc_start: 0.6556 (m-30) cc_final: 0.6290 (t0) REVERT: E 57 MET cc_start: 0.8969 (mtm) cc_final: 0.8319 (mtm) REVERT: E 73 ASP cc_start: 0.9084 (p0) cc_final: 0.8619 (p0) REVERT: E 110 ILE cc_start: 0.9704 (mp) cc_final: 0.8653 (mp) REVERT: E 120 ASN cc_start: 0.7954 (m110) cc_final: 0.7723 (m110) REVERT: E 122 MET cc_start: 0.6660 (ptm) cc_final: 0.5748 (tmm) REVERT: E 132 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8257 (mt-10) REVERT: E 135 GLN cc_start: 0.8858 (tt0) cc_final: 0.8456 (tp-100) REVERT: E 136 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7994 (mm-30) REVERT: E 176 ARG cc_start: 0.8440 (mtt90) cc_final: 0.8219 (mtt90) REVERT: F 112 GLU cc_start: 0.8691 (mp0) cc_final: 0.8409 (mp0) REVERT: G 34 VAL cc_start: 0.9317 (t) cc_final: 0.9017 (p) REVERT: G 73 LYS cc_start: 0.9299 (mttt) cc_final: 0.8882 (mtpp) REVERT: G 80 LYS cc_start: 0.8367 (ttmm) cc_final: 0.7953 (ttmm) REVERT: G 122 ASN cc_start: 0.7847 (t0) cc_final: 0.7589 (p0) REVERT: G 131 MET cc_start: 0.8901 (ppp) cc_final: 0.8641 (tmm) REVERT: G 157 ILE cc_start: 0.9154 (tp) cc_final: 0.8951 (tp) REVERT: G 158 TYR cc_start: 0.8677 (m-80) cc_final: 0.7536 (m-80) REVERT: G 165 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7365 (tm-30) REVERT: H 16 ASP cc_start: 0.8434 (t0) cc_final: 0.8179 (t0) REVERT: H 41 ASP cc_start: 0.9066 (m-30) cc_final: 0.8494 (m-30) REVERT: H 121 LEU cc_start: 0.9198 (mt) cc_final: 0.8657 (mm) REVERT: H 122 MET cc_start: 0.8812 (ttp) cc_final: 0.8524 (tmm) REVERT: I 13 MET cc_start: 0.8397 (ttm) cc_final: 0.7768 (tpp) REVERT: I 85 PHE cc_start: 0.8696 (p90) cc_final: 0.8217 (p90) REVERT: I 87 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: I 96 ASN cc_start: 0.7529 (t0) cc_final: 0.7220 (t0) REVERT: J 19 ASP cc_start: 0.8627 (p0) cc_final: 0.8264 (p0) REVERT: K 101 LEU cc_start: 0.9593 (tp) cc_final: 0.9369 (tp) REVERT: L 30 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8390 (mttt) REVERT: L 66 MET cc_start: 0.8969 (tpp) cc_final: 0.8535 (tpp) REVERT: L 67 ILE cc_start: 0.9142 (mt) cc_final: 0.8474 (tp) REVERT: V 39 ARG cc_start: 0.8188 (ttp-170) cc_final: 0.7976 (ptp-110) REVERT: V 82 TYR cc_start: 0.6995 (m-80) cc_final: 0.6777 (m-80) REVERT: W 227 TRP cc_start: 0.7550 (m-90) cc_final: 0.6937 (m-90) REVERT: W 529 ASP cc_start: 0.8799 (m-30) cc_final: 0.8574 (t0) REVERT: W 541 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8504 (tpp80) REVERT: W 585 ASP cc_start: 0.7973 (t0) cc_final: 0.7689 (t0) REVERT: W 603 GLN cc_start: 0.9033 (tt0) cc_final: 0.8448 (tp-100) REVERT: W 641 LEU cc_start: 0.8179 (mm) cc_final: 0.7660 (mm) REVERT: W 648 GLN cc_start: 0.9155 (tt0) cc_final: 0.8379 (tm-30) REVERT: W 663 THR cc_start: 0.8354 (m) cc_final: 0.8132 (t) REVERT: W 697 VAL cc_start: 0.8807 (p) cc_final: 0.8484 (m) REVERT: W 777 ARG cc_start: 0.6678 (mmm160) cc_final: 0.6180 (ptp90) REVERT: W 796 LEU cc_start: 0.8415 (mt) cc_final: 0.8206 (mm) REVERT: W 804 TRP cc_start: 0.5982 (m100) cc_final: 0.5166 (m100) REVERT: m 310 PHE cc_start: 0.8702 (m-80) cc_final: 0.8257 (m-10) REVERT: m 338 LEU cc_start: 0.8666 (mt) cc_final: 0.8118 (mt) REVERT: m 341 GLU cc_start: 0.7730 (tp30) cc_final: 0.7449 (pt0) REVERT: m 620 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6099 (mp0) REVERT: m 789 ASP cc_start: 0.7838 (m-30) cc_final: 0.7293 (p0) REVERT: m 796 PHE cc_start: 0.6524 (m-10) cc_final: 0.6213 (m-80) REVERT: m 807 ASP cc_start: 0.9501 (t0) cc_final: 0.9184 (m-30) REVERT: m 812 TYR cc_start: 0.9075 (t80) cc_final: 0.8839 (t80) REVERT: m 818 ILE cc_start: 0.6809 (mm) cc_final: 0.6166 (pt) REVERT: m 841 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8485 (pt0) REVERT: m 842 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8708 (tp) REVERT: m 845 GLU cc_start: 0.8688 (tp30) cc_final: 0.8144 (mm-30) REVERT: m 912 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7220 (pp30) REVERT: m 976 TYR cc_start: 0.9147 (m-80) cc_final: 0.8619 (m-80) REVERT: m 1152 GLN cc_start: 0.9484 (tt0) cc_final: 0.9180 (tp-100) REVERT: m 1166 MET cc_start: 0.8484 (mmm) cc_final: 0.7807 (mtp) REVERT: m 1173 ARG cc_start: 0.5729 (ttt180) cc_final: 0.4829 (ptm160) REVERT: m 1180 MET cc_start: 0.7938 (tpp) cc_final: 0.7591 (tpp) REVERT: m 1230 CYS cc_start: 0.8743 (p) cc_final: 0.8250 (t) REVERT: n 200 ARG cc_start: 0.7064 (ttt180) cc_final: 0.6053 (mmt90) REVERT: n 258 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5799 (mttp) REVERT: q 338 TRP cc_start: 0.6421 (m100) cc_final: 0.6098 (m100) REVERT: q 373 TYR cc_start: 0.4509 (t80) cc_final: 0.4098 (t80) REVERT: q 720 PHE cc_start: 0.9246 (m-80) cc_final: 0.8951 (m-80) REVERT: q 763 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9115 (mm-30) REVERT: q 766 MET cc_start: 0.9290 (ttm) cc_final: 0.9079 (mmt) REVERT: q 773 LEU cc_start: 0.8224 (tp) cc_final: 0.7836 (tp) REVERT: q 775 VAL cc_start: 0.7627 (t) cc_final: 0.7417 (p) REVERT: q 777 GLU cc_start: 0.8371 (tp30) cc_final: 0.7976 (mm-30) REVERT: q 789 ARG cc_start: 0.6512 (tpp80) cc_final: 0.6133 (mmm160) REVERT: q 847 LYS cc_start: 0.7873 (pptt) cc_final: 0.7521 (tppt) REVERT: q 849 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7254 (tpm170) REVERT: q 911 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6814 (mm-30) REVERT: r 329 MET cc_start: -0.3405 (tmm) cc_final: -0.3693 (ttp) REVERT: r 401 SER cc_start: 0.9132 (m) cc_final: 0.8845 (p) REVERT: u 106 TRP cc_start: 0.3412 (m-10) cc_final: 0.3209 (m-10) REVERT: u 171 ILE cc_start: 0.4496 (mm) cc_final: 0.4077 (tp) REVERT: u 192 THR cc_start: 0.8059 (m) cc_final: 0.7753 (p) REVERT: u 247 TYR cc_start: 0.8449 (m-80) cc_final: 0.8146 (m-10) REVERT: u 256 ASP cc_start: 0.7995 (t0) cc_final: 0.7348 (t0) REVERT: u 262 ARG cc_start: 0.8655 (ptp90) cc_final: 0.8395 (ptt90) REVERT: u 265 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8983 (mm-30) REVERT: u 268 GLU cc_start: 0.8030 (mm-30) cc_final: 0.6762 (tp30) REVERT: u 269 ASN cc_start: 0.9233 (m-40) cc_final: 0.8908 (m110) REVERT: u 272 TYR cc_start: 0.8166 (m-80) cc_final: 0.7106 (m-80) REVERT: v 49 LEU cc_start: 0.8502 (tp) cc_final: 0.8173 (pp) REVERT: v 63 MET cc_start: 0.5542 (mmm) cc_final: 0.4024 (ptm) REVERT: v 252 PHE cc_start: 0.8681 (m-80) cc_final: 0.8353 (m-80) REVERT: x 240 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6217 (mt-10) REVERT: x 268 ASN cc_start: 0.7507 (t0) cc_final: 0.7047 (p0) REVERT: x 313 TYR cc_start: 0.8394 (t80) cc_final: 0.7672 (t80) REVERT: x 316 TYR cc_start: 0.7664 (m-80) cc_final: 0.7442 (m-80) REVERT: x 336 ASP cc_start: 0.6521 (t0) cc_final: 0.6268 (t0) REVERT: x 348 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8000 (tt0) REVERT: x 352 ASP cc_start: 0.8378 (m-30) cc_final: 0.7999 (m-30) REVERT: j 586 ILE cc_start: 0.3493 (OUTLIER) cc_final: 0.2955 (tp) REVERT: j 652 MET cc_start: -0.3977 (mmt) cc_final: -0.4482 (mtm) REVERT: j 722 PRO cc_start: 0.2914 (Cg_endo) cc_final: 0.2657 (Cg_exo) REVERT: j 788 LYS cc_start: 0.5015 (mttt) cc_final: 0.4544 (ttpt) REVERT: k 21 ARG cc_start: 0.4864 (mtt180) cc_final: 0.4495 (ptt180) REVERT: k 70 ARG cc_start: 0.1658 (mtt180) cc_final: 0.1210 (tpt170) REVERT: k 86 GLN cc_start: 0.7158 (mt0) cc_final: 0.6585 (pp30) REVERT: k 329 TYR cc_start: -0.0711 (m-10) cc_final: -0.1026 (m-10) REVERT: k 398 ILE cc_start: 0.0508 (mt) cc_final: 0.0251 (mt) outliers start: 228 outliers final: 143 residues processed: 2076 average time/residue: 0.7620 time to fit residues: 2674.5875 Evaluate side-chains 1868 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1717 time to evaluate : 7.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1448 ILE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1170 SER Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 629 LEU Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 418 VAL Chi-restraints excluded: chain m residue 444 ASP Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 549 SER Chi-restraints excluded: chain m residue 598 SER Chi-restraints excluded: chain m residue 842 LEU Chi-restraints excluded: chain m residue 904 CYS Chi-restraints excluded: chain m residue 912 GLN Chi-restraints excluded: chain m residue 927 SER Chi-restraints excluded: chain m residue 928 LEU Chi-restraints excluded: chain m residue 950 ILE Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 989 ILE Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain m residue 1122 SER Chi-restraints excluded: chain m residue 1183 SER Chi-restraints excluded: chain m residue 1209 VAL Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 162 GLN Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 258 LYS Chi-restraints excluded: chain n residue 269 VAL Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 250 ASN Chi-restraints excluded: chain q residue 294 HIS Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 878 LYS Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 339 VAL Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 200 VAL Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 231 HIS Chi-restraints excluded: chain v residue 31 LYS Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 586 ILE Chi-restraints excluded: chain j residue 720 PHE Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 875 VAL Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain k residue 77 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 485 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 chunk 726 optimal weight: 6.9990 chunk 594 optimal weight: 50.0000 chunk 240 optimal weight: 2.9990 chunk 874 optimal weight: 20.0000 chunk 944 optimal weight: 40.0000 chunk 778 optimal weight: 40.0000 chunk 866 optimal weight: 8.9990 chunk 298 optimal weight: 20.0000 chunk 701 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 317 GLN A 340 ASN A 480 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 GLN A1390 HIS B 246 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 252 GLN E 178 GLN H 44 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** M 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 100 GLN ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 259 GLN m 329 ASN m 386 ASN ** m 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 912 GLN ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 210 ASN ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 187 GLN ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 319 ASN q 328 ASN ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 921 GLN r 493 ASN v 183 GLN v 244 ASN ** v 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN j 589 ASN ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 734 HIS k 34 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 83688 Z= 0.427 Angle : 0.668 9.784 114048 Z= 0.355 Chirality : 0.044 0.224 12699 Planarity : 0.005 0.067 13884 Dihedral : 15.815 135.110 13291 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.96 % Rotamer: Outliers : 3.70 % Allowed : 13.90 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 9398 helix: 1.63 (0.08), residues: 4139 sheet: 0.10 (0.13), residues: 1375 loop : -0.12 (0.10), residues: 3884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP m 249 HIS 0.009 0.001 HIS B1076 PHE 0.028 0.002 PHE u 126 TYR 0.035 0.002 TYR q 762 ARG 0.009 0.001 ARG m 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2109 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1796 time to evaluate : 6.927 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: A 36 GLU cc_start: 0.8373 (pm20) cc_final: 0.7637 (pm20) REVERT: A 37 TYR cc_start: 0.8763 (m-80) cc_final: 0.8019 (m-10) REVERT: A 39 GLU cc_start: 0.8714 (mp0) cc_final: 0.7872 (tp30) REVERT: A 54 ASN cc_start: 0.9162 (m110) cc_final: 0.8806 (m110) REVERT: A 72 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8120 (mp0) REVERT: A 115 LEU cc_start: 0.8211 (mt) cc_final: 0.7732 (mp) REVERT: A 116 ASP cc_start: 0.7868 (m-30) cc_final: 0.7618 (p0) REVERT: A 146 MET cc_start: 0.8784 (ppp) cc_final: 0.7817 (tmm) REVERT: A 272 LYS cc_start: 0.9366 (ttmt) cc_final: 0.9072 (mttt) REVERT: A 282 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7965 (ptp) REVERT: A 283 ASP cc_start: 0.7634 (m-30) cc_final: 0.7241 (m-30) REVERT: A 298 GLN cc_start: 0.8788 (tp40) cc_final: 0.8150 (tp40) REVERT: A 306 ASP cc_start: 0.8735 (t0) cc_final: 0.8150 (t0) REVERT: A 309 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8912 (mt) REVERT: A 349 SER cc_start: 0.9606 (p) cc_final: 0.9331 (p) REVERT: A 432 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9146 (mmmm) REVERT: A 457 MET cc_start: 0.8913 (mtm) cc_final: 0.8664 (mtp) REVERT: A 466 TYR cc_start: 0.8971 (m-80) cc_final: 0.8058 (m-80) REVERT: A 527 ASP cc_start: 0.8266 (p0) cc_final: 0.7823 (p0) REVERT: A 535 MET cc_start: 0.9134 (ttt) cc_final: 0.8897 (ttm) REVERT: A 540 THR cc_start: 0.9443 (m) cc_final: 0.9206 (p) REVERT: A 606 MET cc_start: 0.8585 (tpp) cc_final: 0.8206 (tpp) REVERT: A 610 ASP cc_start: 0.8737 (t0) cc_final: 0.8377 (t0) REVERT: A 617 VAL cc_start: 0.9485 (t) cc_final: 0.9226 (p) REVERT: A 712 ARG cc_start: 0.8854 (ttm110) cc_final: 0.8650 (ttm170) REVERT: A 728 ASP cc_start: 0.8783 (m-30) cc_final: 0.8507 (m-30) REVERT: A 769 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8881 (mm-40) REVERT: A 770 MET cc_start: 0.8568 (tpp) cc_final: 0.8289 (tpp) REVERT: A 813 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8000 (mt-10) REVERT: A 847 GLU cc_start: 0.8379 (pt0) cc_final: 0.8121 (pt0) REVERT: A 863 ASP cc_start: 0.8911 (m-30) cc_final: 0.8546 (m-30) REVERT: A 971 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8680 (tm-30) REVERT: A 1073 SER cc_start: 0.9452 (m) cc_final: 0.8996 (p) REVERT: A 1207 LYS cc_start: 0.9468 (mmtt) cc_final: 0.9213 (mmtm) REVERT: A 1211 MET cc_start: 0.7867 (mmm) cc_final: 0.6967 (mmm) REVERT: A 1217 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9070 (mmmm) REVERT: A 1284 LYS cc_start: 0.8804 (tptt) cc_final: 0.8307 (ttmm) REVERT: A 1354 GLU cc_start: 0.8508 (tp30) cc_final: 0.8183 (tp30) REVERT: A 1453 LEU cc_start: 0.9501 (mt) cc_final: 0.9298 (tp) REVERT: B 14 THR cc_start: 0.9315 (m) cc_final: 0.9106 (p) REVERT: B 35 LEU cc_start: 0.9211 (mt) cc_final: 0.8825 (mm) REVERT: B 39 ASP cc_start: 0.8269 (m-30) cc_final: 0.7997 (m-30) REVERT: B 182 LYS cc_start: 0.9492 (mttt) cc_final: 0.9132 (mtmm) REVERT: B 183 MET cc_start: 0.8939 (mmm) cc_final: 0.8659 (mmm) REVERT: B 199 SER cc_start: 0.9517 (t) cc_final: 0.9163 (p) REVERT: B 233 SER cc_start: 0.9378 (m) cc_final: 0.9065 (t) REVERT: B 269 LYS cc_start: 0.8983 (mttm) cc_final: 0.8693 (mtpt) REVERT: B 270 GLN cc_start: 0.8653 (mm110) cc_final: 0.8361 (mm110) REVERT: B 312 GLU cc_start: 0.8511 (tt0) cc_final: 0.8256 (tt0) REVERT: B 343 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8805 (mm-40) REVERT: B 360 GLU cc_start: 0.8877 (pm20) cc_final: 0.8519 (pm20) REVERT: B 363 PHE cc_start: 0.8365 (m-80) cc_final: 0.8054 (m-80) REVERT: B 384 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8539 (mp0) REVERT: B 492 ASN cc_start: 0.9570 (t0) cc_final: 0.9214 (t0) REVERT: B 519 GLU cc_start: 0.7194 (tt0) cc_final: 0.6478 (tm-30) REVERT: B 531 ASN cc_start: 0.8281 (m-40) cc_final: 0.6488 (m110) REVERT: B 550 PHE cc_start: 0.8932 (m-80) cc_final: 0.8576 (m-80) REVERT: B 573 ILE cc_start: 0.9670 (mt) cc_final: 0.9444 (mp) REVERT: B 595 ASP cc_start: 0.8414 (m-30) cc_final: 0.7950 (m-30) REVERT: B 611 ASP cc_start: 0.8192 (t0) cc_final: 0.7703 (t0) REVERT: B 656 GLN cc_start: 0.8686 (mt0) cc_final: 0.8432 (mt0) REVERT: B 691 ASP cc_start: 0.8893 (p0) cc_final: 0.8561 (p0) REVERT: B 706 ASP cc_start: 0.9053 (m-30) cc_final: 0.8795 (m-30) REVERT: B 754 SER cc_start: 0.9485 (m) cc_final: 0.9263 (m) REVERT: B 835 GLN cc_start: 0.8109 (mt0) cc_final: 0.7716 (mp10) REVERT: B 863 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 875 GLU cc_start: 0.8380 (pp20) cc_final: 0.8089 (pp20) REVERT: B 884 ARG cc_start: 0.7178 (mmt-90) cc_final: 0.6876 (mmt-90) REVERT: B 904 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7131 (ttt-90) REVERT: B 923 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8484 (tt0) REVERT: B 924 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8811 (pm20) REVERT: B 931 TYR cc_start: 0.8962 (p90) cc_final: 0.8513 (p90) REVERT: B 1020 ARG cc_start: 0.8817 (mtt-85) cc_final: 0.8426 (mtt-85) REVERT: B 1153 GLU cc_start: 0.7961 (mp0) cc_final: 0.7575 (mp0) REVERT: B 1168 LEU cc_start: 0.9425 (mt) cc_final: 0.9170 (mp) REVERT: D 38 GLN cc_start: 0.8429 (mm-40) cc_final: 0.7933 (mp10) REVERT: D 137 LEU cc_start: 0.7524 (mt) cc_final: 0.7298 (tp) REVERT: D 138 HIS cc_start: 0.8235 (t-90) cc_final: 0.7529 (t-90) REVERT: D 144 GLN cc_start: 0.9405 (mm-40) cc_final: 0.8923 (tp-100) REVERT: D 183 ASP cc_start: 0.6550 (m-30) cc_final: 0.6292 (t0) REVERT: E 20 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: E 24 ASP cc_start: 0.8441 (m-30) cc_final: 0.8113 (m-30) REVERT: E 33 GLU cc_start: 0.8737 (tp30) cc_final: 0.8254 (tp30) REVERT: E 55 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8271 (mmtm) REVERT: E 57 MET cc_start: 0.9023 (mtm) cc_final: 0.8336 (mpp) REVERT: E 73 ASP cc_start: 0.9185 (p0) cc_final: 0.8534 (p0) REVERT: E 110 ILE cc_start: 0.9666 (mp) cc_final: 0.8711 (mp) REVERT: E 120 ASN cc_start: 0.8171 (m110) cc_final: 0.7928 (m110) REVERT: E 135 GLN cc_start: 0.8931 (tt0) cc_final: 0.8628 (tp-100) REVERT: E 136 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8146 (mm-30) REVERT: F 112 GLU cc_start: 0.8840 (mp0) cc_final: 0.8606 (mp0) REVERT: G 29 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8355 (ttmt) REVERT: G 34 VAL cc_start: 0.9315 (t) cc_final: 0.9042 (p) REVERT: G 73 LYS cc_start: 0.9347 (mttt) cc_final: 0.8996 (mtpp) REVERT: G 80 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8551 (ttmt) REVERT: G 157 ILE cc_start: 0.9128 (tp) cc_final: 0.8927 (tp) REVERT: G 165 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7466 (tm-30) REVERT: H 41 ASP cc_start: 0.9041 (m-30) cc_final: 0.8572 (m-30) REVERT: H 56 THR cc_start: 0.8815 (m) cc_final: 0.8305 (p) REVERT: H 121 LEU cc_start: 0.9177 (mt) cc_final: 0.8824 (mm) REVERT: H 122 MET cc_start: 0.8821 (ttp) cc_final: 0.8339 (tmm) REVERT: I 13 MET cc_start: 0.8345 (ttm) cc_final: 0.7570 (tpp) REVERT: I 85 PHE cc_start: 0.8713 (p90) cc_final: 0.8402 (p90) REVERT: I 96 ASN cc_start: 0.7631 (t0) cc_final: 0.7320 (t0) REVERT: J 19 ASP cc_start: 0.8660 (p0) cc_final: 0.8442 (p0) REVERT: K 101 LEU cc_start: 0.9580 (tp) cc_final: 0.9378 (tp) REVERT: L 30 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8383 (mttt) REVERT: V 9 GLU cc_start: 0.6812 (tp30) cc_final: 0.5756 (tp30) REVERT: W 227 TRP cc_start: 0.7025 (m-90) cc_final: 0.5826 (m-90) REVERT: W 529 ASP cc_start: 0.8820 (m-30) cc_final: 0.8619 (t70) REVERT: W 540 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7655 (m) REVERT: W 556 GLU cc_start: 0.8103 (tp30) cc_final: 0.7790 (tm-30) REVERT: W 565 ILE cc_start: 0.8919 (mt) cc_final: 0.8556 (tp) REVERT: W 578 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.6908 (p0) REVERT: W 585 ASP cc_start: 0.8175 (t0) cc_final: 0.7792 (t0) REVERT: W 603 GLN cc_start: 0.9207 (tt0) cc_final: 0.8602 (tp-100) REVERT: W 641 LEU cc_start: 0.8183 (mm) cc_final: 0.7708 (mm) REVERT: W 663 THR cc_start: 0.8305 (m) cc_final: 0.8072 (t) REVERT: W 687 ARG cc_start: 0.8775 (ttp-170) cc_final: 0.8547 (ttp-110) REVERT: W 697 VAL cc_start: 0.8674 (p) cc_final: 0.8381 (m) REVERT: W 777 ARG cc_start: 0.7218 (mmm160) cc_final: 0.6383 (ptp90) REVERT: W 804 TRP cc_start: 0.6554 (m100) cc_final: 0.5799 (m100) REVERT: m 310 PHE cc_start: 0.8628 (m-80) cc_final: 0.8284 (m-10) REVERT: m 313 TYR cc_start: 0.7583 (m-80) cc_final: 0.7271 (m-80) REVERT: m 338 LEU cc_start: 0.8602 (mt) cc_final: 0.8165 (mt) REVERT: m 341 GLU cc_start: 0.7632 (tp30) cc_final: 0.7318 (pt0) REVERT: m 466 ILE cc_start: 0.5970 (OUTLIER) cc_final: 0.5324 (pt) REVERT: m 612 GLN cc_start: 0.7803 (pp30) cc_final: 0.7602 (pp30) REVERT: m 619 ILE cc_start: 0.7402 (tt) cc_final: 0.6757 (tt) REVERT: m 620 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6061 (mp0) REVERT: m 669 ASN cc_start: 0.8500 (m110) cc_final: 0.7943 (p0) REVERT: m 789 ASP cc_start: 0.7700 (m-30) cc_final: 0.7444 (p0) REVERT: m 796 PHE cc_start: 0.6926 (m-10) cc_final: 0.6710 (m-80) REVERT: m 807 ASP cc_start: 0.9534 (t0) cc_final: 0.9141 (m-30) REVERT: m 812 TYR cc_start: 0.9120 (t80) cc_final: 0.8820 (t80) REVERT: m 818 ILE cc_start: 0.7220 (mm) cc_final: 0.6755 (pt) REVERT: m 882 ARG cc_start: 0.8962 (ttm110) cc_final: 0.8323 (ttm110) REVERT: m 909 LYS cc_start: 0.8272 (mttt) cc_final: 0.7994 (mmmm) REVERT: m 912 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.7013 (pp30) REVERT: m 1152 GLN cc_start: 0.9453 (tt0) cc_final: 0.9204 (tp-100) REVERT: m 1166 MET cc_start: 0.8503 (mmm) cc_final: 0.7820 (mtp) REVERT: m 1173 ARG cc_start: 0.5884 (ttt180) cc_final: 0.4947 (ptm160) REVERT: m 1230 CYS cc_start: 0.8766 (p) cc_final: 0.8141 (t) REVERT: n 153 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6781 (pp20) REVERT: n 200 ARG cc_start: 0.6972 (ttt180) cc_final: 0.6059 (mmt90) REVERT: n 233 ILE cc_start: 0.8860 (pt) cc_final: 0.8154 (pt) REVERT: q 1 MET cc_start: 0.2509 (mmp) cc_final: 0.1663 (ttp) REVERT: q 338 TRP cc_start: 0.6474 (m100) cc_final: 0.6174 (m100) REVERT: q 373 TYR cc_start: 0.4965 (t80) cc_final: 0.4757 (t80) REVERT: q 467 LYS cc_start: 0.5799 (mtpt) cc_final: 0.4738 (tptp) REVERT: q 720 PHE cc_start: 0.9165 (m-80) cc_final: 0.8859 (m-80) REVERT: q 773 LEU cc_start: 0.8122 (tp) cc_final: 0.7685 (tp) REVERT: q 777 GLU cc_start: 0.8450 (tp30) cc_final: 0.7991 (mm-30) REVERT: q 789 ARG cc_start: 0.6369 (tpp80) cc_final: 0.6094 (mtp180) REVERT: q 847 LYS cc_start: 0.8117 (pptt) cc_final: 0.7773 (tppt) REVERT: q 849 ARG cc_start: 0.7836 (ttt180) cc_final: 0.7222 (tpm170) REVERT: r 329 MET cc_start: -0.3308 (tmm) cc_final: -0.3620 (ttp) REVERT: r 373 ASP cc_start: 0.8236 (t0) cc_final: 0.7949 (t0) REVERT: r 401 SER cc_start: 0.9123 (m) cc_final: 0.8761 (p) REVERT: u 90 LEU cc_start: 0.7373 (mm) cc_final: 0.7079 (tp) REVERT: u 171 ILE cc_start: 0.4415 (mm) cc_final: 0.3766 (pt) REVERT: u 265 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9072 (mm-30) REVERT: u 269 ASN cc_start: 0.9355 (m-40) cc_final: 0.9010 (m-40) REVERT: u 272 TYR cc_start: 0.8195 (m-80) cc_final: 0.7235 (m-80) REVERT: v 48 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7865 (ttp80) REVERT: v 167 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6350 (tp30) REVERT: v 200 PHE cc_start: 0.7883 (t80) cc_final: 0.7596 (t80) REVERT: v 252 PHE cc_start: 0.8737 (m-80) cc_final: 0.8315 (m-80) REVERT: x 135 ASP cc_start: 0.3971 (m-30) cc_final: 0.3611 (t0) REVERT: x 233 LYS cc_start: 0.8142 (pttt) cc_final: 0.7797 (pttm) REVERT: x 240 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6165 (mt-10) REVERT: x 268 ASN cc_start: 0.7373 (t0) cc_final: 0.6803 (p0) REVERT: x 313 TYR cc_start: 0.8439 (t80) cc_final: 0.7889 (t80) REVERT: x 336 ASP cc_start: 0.6389 (t0) cc_final: 0.5601 (t0) REVERT: x 348 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7947 (tt0) REVERT: x 352 ASP cc_start: 0.8339 (m-30) cc_final: 0.7889 (m-30) REVERT: k 21 ARG cc_start: 0.4906 (mtt180) cc_final: 0.4544 (ptt180) REVERT: k 70 ARG cc_start: 0.1349 (mtt180) cc_final: 0.0785 (tpt170) REVERT: k 86 GLN cc_start: 0.7183 (mt0) cc_final: 0.6682 (pp30) outliers start: 313 outliers final: 225 residues processed: 1968 average time/residue: 0.7645 time to fit residues: 2561.4831 Evaluate side-chains 1892 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1658 time to evaluate : 6.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 996 CYS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1069 ILE Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 LYS Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1448 ILE Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1148 LYS Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 130 SER Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 522 THR Chi-restraints excluded: chain W residue 540 VAL Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 609 VAL Chi-restraints excluded: chain W residue 629 LEU Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 461 SER Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 466 ILE Chi-restraints excluded: chain m residue 549 SER Chi-restraints excluded: chain m residue 646 ILE Chi-restraints excluded: chain m residue 650 THR Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 851 GLU Chi-restraints excluded: chain m residue 912 GLN Chi-restraints excluded: chain m residue 927 SER Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 1023 VAL Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain m residue 1183 SER Chi-restraints excluded: chain m residue 1199 GLU Chi-restraints excluded: chain m residue 1209 VAL Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 190 LEU Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 223 LEU Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 83 ILE Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 294 HIS Chi-restraints excluded: chain q residue 328 ASN Chi-restraints excluded: chain q residue 489 PHE Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 695 LEU Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain q residue 878 LYS Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 208 ILE Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain v residue 136 ASP Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 333 ILE Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 342 SER Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 720 PHE Chi-restraints excluded: chain j residue 734 HIS Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 875 VAL Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain k residue 53 SER Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 358 SER Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 863 optimal weight: 30.0000 chunk 657 optimal weight: 30.0000 chunk 453 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 417 optimal weight: 30.0000 chunk 587 optimal weight: 20.0000 chunk 877 optimal weight: 30.0000 chunk 928 optimal weight: 8.9990 chunk 458 optimal weight: 7.9990 chunk 831 optimal weight: 0.4980 chunk 250 optimal weight: 0.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 295 GLN A 480 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 386 ASN ** m 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 912 GLN ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 483 ASN r 340 ASN ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 310 HIS ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 500 HIS ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 83688 Z= 0.329 Angle : 0.616 13.634 114048 Z= 0.326 Chirality : 0.043 0.298 12699 Planarity : 0.004 0.059 13884 Dihedral : 15.832 134.718 13291 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.11 % Favored : 96.88 % Rotamer: Outliers : 3.74 % Allowed : 15.51 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 9398 helix: 1.69 (0.08), residues: 4153 sheet: 0.06 (0.13), residues: 1384 loop : -0.15 (0.10), residues: 3861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP m 333 HIS 0.015 0.001 HIS j 734 PHE 0.024 0.002 PHE q 713 TYR 0.030 0.002 TYR q 762 ARG 0.014 0.001 ARG q 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2100 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1784 time to evaluate : 7.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8164 (mt-10) REVERT: A 39 GLU cc_start: 0.8408 (mp0) cc_final: 0.7680 (tp30) REVERT: A 50 GLU cc_start: 0.8142 (pp20) cc_final: 0.7861 (pp20) REVERT: A 54 ASN cc_start: 0.9127 (m110) cc_final: 0.8857 (m110) REVERT: A 72 GLU cc_start: 0.8562 (mm-30) cc_final: 0.7990 (mp0) REVERT: A 115 LEU cc_start: 0.8224 (mt) cc_final: 0.7724 (mp) REVERT: A 116 ASP cc_start: 0.7943 (m-30) cc_final: 0.7597 (p0) REVERT: A 145 LYS cc_start: 0.7922 (tptt) cc_final: 0.7309 (tptp) REVERT: A 146 MET cc_start: 0.8886 (ppp) cc_final: 0.8138 (tmm) REVERT: A 222 ARG cc_start: 0.8477 (mtt90) cc_final: 0.8229 (mpt90) REVERT: A 272 LYS cc_start: 0.9353 (ttmt) cc_final: 0.9061 (mttt) REVERT: A 282 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8021 (ptp) REVERT: A 283 ASP cc_start: 0.7955 (m-30) cc_final: 0.7537 (m-30) REVERT: A 298 GLN cc_start: 0.8723 (tp40) cc_final: 0.8102 (tp40) REVERT: A 306 ASP cc_start: 0.8571 (t0) cc_final: 0.8095 (t0) REVERT: A 309 ILE cc_start: 0.9116 (mt) cc_final: 0.8893 (mt) REVERT: A 454 MET cc_start: 0.8792 (mpp) cc_final: 0.8226 (mpp) REVERT: A 457 MET cc_start: 0.8934 (mtm) cc_final: 0.8601 (mtp) REVERT: A 466 TYR cc_start: 0.8978 (m-80) cc_final: 0.7985 (m-80) REVERT: A 527 ASP cc_start: 0.7997 (p0) cc_final: 0.7201 (p0) REVERT: A 535 MET cc_start: 0.9214 (ttt) cc_final: 0.8796 (ttp) REVERT: A 540 THR cc_start: 0.9430 (m) cc_final: 0.9196 (p) REVERT: A 551 LEU cc_start: 0.9467 (mt) cc_final: 0.9241 (mt) REVERT: A 606 MET cc_start: 0.8609 (tpp) cc_final: 0.8092 (tpp) REVERT: A 617 VAL cc_start: 0.9467 (t) cc_final: 0.9227 (p) REVERT: A 712 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8589 (ttm170) REVERT: A 728 ASP cc_start: 0.8736 (m-30) cc_final: 0.8489 (m-30) REVERT: A 770 MET cc_start: 0.8525 (tpp) cc_final: 0.8249 (tpp) REVERT: A 813 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 863 ASP cc_start: 0.8888 (m-30) cc_final: 0.8540 (m-30) REVERT: A 898 TYR cc_start: 0.8596 (m-80) cc_final: 0.7959 (m-80) REVERT: A 971 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8634 (tm-30) REVERT: A 1073 SER cc_start: 0.9474 (m) cc_final: 0.8992 (p) REVERT: A 1207 LYS cc_start: 0.9559 (mmtt) cc_final: 0.9246 (mmtm) REVERT: A 1211 MET cc_start: 0.7738 (mmm) cc_final: 0.6995 (mmm) REVERT: A 1217 LYS cc_start: 0.9430 (mmtt) cc_final: 0.9038 (mmmm) REVERT: A 1222 PHE cc_start: 0.7587 (m-80) cc_final: 0.7270 (m-80) REVERT: A 1284 LYS cc_start: 0.8803 (tptt) cc_final: 0.8291 (ttmm) REVERT: A 1354 GLU cc_start: 0.8480 (tp30) cc_final: 0.8231 (tp30) REVERT: A 1389 ARG cc_start: 0.8657 (ptt-90) cc_final: 0.8256 (ptt-90) REVERT: A 1394 ARG cc_start: 0.7843 (mpt180) cc_final: 0.7623 (mpt180) REVERT: A 1447 MET cc_start: 0.9024 (mmm) cc_final: 0.8755 (mmm) REVERT: A 1453 LEU cc_start: 0.9547 (mt) cc_final: 0.9345 (tp) REVERT: B 35 LEU cc_start: 0.9159 (mt) cc_final: 0.8831 (mm) REVERT: B 39 ASP cc_start: 0.8207 (m-30) cc_final: 0.7953 (m-30) REVERT: B 43 GLU cc_start: 0.7889 (tp30) cc_final: 0.7665 (tp30) REVERT: B 89 MET cc_start: 0.7340 (tpt) cc_final: 0.7051 (tpt) REVERT: B 182 LYS cc_start: 0.9467 (mttt) cc_final: 0.9033 (mtmm) REVERT: B 233 SER cc_start: 0.9384 (m) cc_final: 0.9094 (t) REVERT: B 250 TYR cc_start: 0.8549 (m-80) cc_final: 0.8291 (m-80) REVERT: B 269 LYS cc_start: 0.8952 (mttm) cc_final: 0.8603 (mtpt) REVERT: B 270 GLN cc_start: 0.8726 (mm110) cc_final: 0.8325 (mm110) REVERT: B 291 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8594 (mm110) REVERT: B 312 GLU cc_start: 0.8477 (tt0) cc_final: 0.8254 (tt0) REVERT: B 343 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8739 (mm-40) REVERT: B 360 GLU cc_start: 0.8895 (pm20) cc_final: 0.8219 (pm20) REVERT: B 363 PHE cc_start: 0.8268 (m-80) cc_final: 0.7553 (m-80) REVERT: B 384 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8665 (mp0) REVERT: B 419 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7413 (ttp-170) REVERT: B 485 LEU cc_start: 0.9839 (mt) cc_final: 0.9590 (mt) REVERT: B 492 ASN cc_start: 0.9570 (t0) cc_final: 0.9229 (t0) REVERT: B 519 GLU cc_start: 0.7056 (tt0) cc_final: 0.6466 (tm-30) REVERT: B 531 ASN cc_start: 0.8224 (m-40) cc_final: 0.6302 (m110) REVERT: B 550 PHE cc_start: 0.8939 (m-80) cc_final: 0.8525 (m-80) REVERT: B 573 ILE cc_start: 0.9677 (mt) cc_final: 0.9462 (mp) REVERT: B 595 ASP cc_start: 0.8392 (m-30) cc_final: 0.7899 (m-30) REVERT: B 611 ASP cc_start: 0.8224 (t0) cc_final: 0.7831 (t0) REVERT: B 656 GLN cc_start: 0.8634 (mt0) cc_final: 0.8366 (mt0) REVERT: B 691 ASP cc_start: 0.9024 (p0) cc_final: 0.8647 (p0) REVERT: B 706 ASP cc_start: 0.9007 (m-30) cc_final: 0.8752 (m-30) REVERT: B 754 SER cc_start: 0.9512 (m) cc_final: 0.9278 (m) REVERT: B 875 GLU cc_start: 0.8359 (pp20) cc_final: 0.8126 (pp20) REVERT: B 884 ARG cc_start: 0.7205 (mmt-90) cc_final: 0.6864 (mmt-90) REVERT: B 904 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7164 (ttt-90) REVERT: B 923 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8478 (tt0) REVERT: B 924 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: B 931 TYR cc_start: 0.8985 (p90) cc_final: 0.8507 (p90) REVERT: B 1020 ARG cc_start: 0.8748 (mtt-85) cc_final: 0.8240 (mtt-85) REVERT: B 1125 ASP cc_start: 0.8609 (t0) cc_final: 0.8388 (t0) REVERT: B 1139 ILE cc_start: 0.9687 (mt) cc_final: 0.9398 (mm) REVERT: B 1146 PHE cc_start: 0.9183 (t80) cc_final: 0.8929 (t80) REVERT: B 1153 GLU cc_start: 0.7925 (mp0) cc_final: 0.7480 (mp0) REVERT: B 1168 LEU cc_start: 0.9403 (mt) cc_final: 0.9128 (mp) REVERT: B 1192 TYR cc_start: 0.8958 (m-80) cc_final: 0.8756 (m-10) REVERT: C 152 GLU cc_start: 0.7609 (tp30) cc_final: 0.7289 (tp30) REVERT: C 210 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8096 (mm-30) REVERT: D 38 GLN cc_start: 0.8379 (mm-40) cc_final: 0.7647 (mp10) REVERT: D 45 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: D 104 LYS cc_start: 0.9398 (mppt) cc_final: 0.9183 (mmtm) REVERT: D 138 HIS cc_start: 0.8319 (t-90) cc_final: 0.7673 (t-90) REVERT: D 144 GLN cc_start: 0.9433 (mm-40) cc_final: 0.8793 (tp-100) REVERT: D 166 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7920 (mmmt) REVERT: D 183 ASP cc_start: 0.6478 (m-30) cc_final: 0.6197 (t0) REVERT: E 20 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: E 24 ASP cc_start: 0.8388 (m-30) cc_final: 0.8044 (m-30) REVERT: E 33 GLU cc_start: 0.8704 (tp30) cc_final: 0.8153 (tp30) REVERT: E 57 MET cc_start: 0.9018 (mtm) cc_final: 0.8350 (mpp) REVERT: E 73 ASP cc_start: 0.9202 (p0) cc_final: 0.8507 (p0) REVERT: E 135 GLN cc_start: 0.8964 (tt0) cc_final: 0.8516 (tp40) REVERT: G 3 PHE cc_start: 0.8295 (m-80) cc_final: 0.7784 (m-80) REVERT: G 29 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8503 (ttmm) REVERT: G 34 VAL cc_start: 0.9349 (t) cc_final: 0.9083 (p) REVERT: G 73 LYS cc_start: 0.9341 (mttt) cc_final: 0.8920 (mtpp) REVERT: G 80 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8401 (ttmt) REVERT: G 165 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7314 (tm-30) REVERT: H 41 ASP cc_start: 0.9060 (m-30) cc_final: 0.8585 (m-30) REVERT: H 56 THR cc_start: 0.8746 (m) cc_final: 0.8315 (p) REVERT: H 121 LEU cc_start: 0.9188 (mt) cc_final: 0.8834 (mm) REVERT: H 122 MET cc_start: 0.8892 (ttp) cc_final: 0.8494 (tmm) REVERT: I 13 MET cc_start: 0.8367 (ttm) cc_final: 0.7610 (tpp) REVERT: I 85 PHE cc_start: 0.8813 (p90) cc_final: 0.8463 (p90) REVERT: I 96 ASN cc_start: 0.7467 (t0) cc_final: 0.7227 (t0) REVERT: W 227 TRP cc_start: 0.6972 (m-90) cc_final: 0.5365 (m-90) REVERT: W 529 ASP cc_start: 0.8854 (m-30) cc_final: 0.8578 (t70) REVERT: W 540 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7150 (m) REVERT: W 556 GLU cc_start: 0.8075 (tp30) cc_final: 0.7814 (tm-30) REVERT: W 578 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6687 (p0) REVERT: W 585 ASP cc_start: 0.8155 (t0) cc_final: 0.7768 (t0) REVERT: W 603 GLN cc_start: 0.9246 (tt0) cc_final: 0.8625 (tp-100) REVERT: W 641 LEU cc_start: 0.8299 (mm) cc_final: 0.7675 (mm) REVERT: W 663 THR cc_start: 0.8316 (m) cc_final: 0.8073 (t) REVERT: W 687 ARG cc_start: 0.8783 (ttp-170) cc_final: 0.8525 (ttp-110) REVERT: W 697 VAL cc_start: 0.8592 (p) cc_final: 0.8323 (m) REVERT: W 804 TRP cc_start: 0.6389 (m100) cc_final: 0.5680 (m100) REVERT: m 310 PHE cc_start: 0.8709 (m-80) cc_final: 0.8275 (m-10) REVERT: m 341 GLU cc_start: 0.7602 (tp30) cc_final: 0.7296 (pt0) REVERT: m 612 GLN cc_start: 0.7871 (pp30) cc_final: 0.7651 (pp30) REVERT: m 619 ILE cc_start: 0.7681 (tt) cc_final: 0.7323 (tt) REVERT: m 659 MET cc_start: 0.9065 (mmm) cc_final: 0.8633 (mmm) REVERT: m 669 ASN cc_start: 0.8414 (m110) cc_final: 0.8054 (p0) REVERT: m 784 MET cc_start: 0.8601 (tmm) cc_final: 0.8349 (tmm) REVERT: m 789 ASP cc_start: 0.7788 (m-30) cc_final: 0.7501 (p0) REVERT: m 807 ASP cc_start: 0.9505 (t0) cc_final: 0.9196 (m-30) REVERT: m 812 TYR cc_start: 0.8924 (t80) cc_final: 0.8723 (t80) REVERT: m 818 ILE cc_start: 0.6997 (mm) cc_final: 0.6717 (pt) REVERT: m 828 PHE cc_start: 0.8675 (m-10) cc_final: 0.8341 (m-10) REVERT: m 882 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8743 (ttm110) REVERT: m 912 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7221 (pp30) REVERT: m 1152 GLN cc_start: 0.9452 (tt0) cc_final: 0.9209 (tp-100) REVERT: m 1166 MET cc_start: 0.8478 (mmm) cc_final: 0.7768 (mtp) REVERT: m 1230 CYS cc_start: 0.8499 (p) cc_final: 0.7740 (t) REVERT: n 153 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6682 (pp20) REVERT: n 200 ARG cc_start: 0.7018 (ttt180) cc_final: 0.5990 (mmt90) REVERT: q 1 MET cc_start: 0.2286 (mmp) cc_final: 0.1395 (ttp) REVERT: q 338 TRP cc_start: 0.6431 (m100) cc_final: 0.6102 (m100) REVERT: q 597 LEU cc_start: -0.0232 (OUTLIER) cc_final: -0.0495 (tp) REVERT: q 720 PHE cc_start: 0.9169 (m-80) cc_final: 0.8888 (m-80) REVERT: q 847 LYS cc_start: 0.8029 (pptt) cc_final: 0.7683 (tppt) REVERT: q 849 ARG cc_start: 0.7732 (ttt180) cc_final: 0.7496 (ttm170) REVERT: q 873 MET cc_start: 0.7986 (mmt) cc_final: 0.7772 (mmp) REVERT: q 911 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7059 (mm-30) REVERT: q 928 MET cc_start: 0.5743 (ptt) cc_final: 0.5536 (ppp) REVERT: r 318 ASP cc_start: 0.1287 (m-30) cc_final: 0.0769 (t0) REVERT: r 329 MET cc_start: -0.3039 (tmm) cc_final: -0.3360 (ttp) REVERT: r 373 ASP cc_start: 0.8211 (t0) cc_final: 0.7873 (t0) REVERT: r 401 SER cc_start: 0.9088 (m) cc_final: 0.8732 (p) REVERT: u 90 LEU cc_start: 0.7383 (mm) cc_final: 0.7175 (tp) REVERT: u 171 ILE cc_start: 0.4348 (mm) cc_final: 0.3691 (pt) REVERT: u 265 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9086 (mm-30) REVERT: u 269 ASN cc_start: 0.9333 (m-40) cc_final: 0.9118 (m-40) REVERT: v 167 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6242 (tp30) REVERT: v 200 PHE cc_start: 0.7791 (t80) cc_final: 0.7582 (t80) REVERT: v 252 PHE cc_start: 0.8770 (m-80) cc_final: 0.8339 (m-80) REVERT: x 240 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6163 (mt-10) REVERT: x 268 ASN cc_start: 0.7380 (t0) cc_final: 0.6782 (p0) REVERT: x 313 TYR cc_start: 0.8425 (t80) cc_final: 0.7922 (t80) REVERT: x 319 ASP cc_start: 0.7343 (m-30) cc_final: 0.6967 (m-30) REVERT: x 336 ASP cc_start: 0.6116 (t0) cc_final: 0.5742 (t0) REVERT: x 348 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7953 (tt0) REVERT: x 352 ASP cc_start: 0.8530 (m-30) cc_final: 0.8182 (m-30) REVERT: j 541 LYS cc_start: -0.0238 (tmtt) cc_final: -0.1083 (mmmt) REVERT: k 21 ARG cc_start: 0.4775 (mtt180) cc_final: 0.4303 (ptt180) REVERT: k 70 ARG cc_start: 0.1297 (mtt180) cc_final: 0.0765 (tpt170) REVERT: k 86 GLN cc_start: 0.7200 (mt0) cc_final: 0.6647 (pp30) outliers start: 316 outliers final: 238 residues processed: 1949 average time/residue: 0.7556 time to fit residues: 2511.2328 Evaluate side-chains 1908 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1660 time to evaluate : 6.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 996 CYS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 217 LEU Chi-restraints excluded: chain W residue 241 ARG Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 414 VAL Chi-restraints excluded: chain W residue 522 THR Chi-restraints excluded: chain W residue 540 VAL Chi-restraints excluded: chain W residue 541 ARG Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 598 LEU Chi-restraints excluded: chain W residue 609 VAL Chi-restraints excluded: chain W residue 629 LEU Chi-restraints excluded: chain W residue 647 GLN Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 703 ASN Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 294 LEU Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 461 SER Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 542 MET Chi-restraints excluded: chain m residue 549 SER Chi-restraints excluded: chain m residue 598 SER Chi-restraints excluded: chain m residue 650 THR Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 851 GLU Chi-restraints excluded: chain m residue 873 VAL Chi-restraints excluded: chain m residue 880 THR Chi-restraints excluded: chain m residue 912 GLN Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 925 MET Chi-restraints excluded: chain m residue 927 SER Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 1023 VAL Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain m residue 1209 VAL Chi-restraints excluded: chain m residue 1234 LEU Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 185 ILE Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 223 LEU Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 83 ILE Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 200 GLU Chi-restraints excluded: chain q residue 294 HIS Chi-restraints excluded: chain q residue 350 VAL Chi-restraints excluded: chain q residue 597 LEU Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 695 LEU Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain q residue 878 LYS Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain r residue 387 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 145 ILE Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 210 VAL Chi-restraints excluded: chain v residue 257 ILE Chi-restraints excluded: chain v residue 299 HIS Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 713 SER Chi-restraints excluded: chain j residue 720 PHE Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 875 VAL Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain k residue 53 SER Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 172 VAL Chi-restraints excluded: chain k residue 358 SER Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 773 optimal weight: 50.0000 chunk 527 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 691 optimal weight: 20.0000 chunk 383 optimal weight: 0.9990 chunk 792 optimal weight: 20.0000 chunk 642 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 474 optimal weight: 2.9990 chunk 833 optimal weight: 30.0000 chunk 234 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 480 ASN A 526 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN C 64 HIS E 178 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 912 GLN ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 328 ASN q 351 GLN q 482 ASN q 526 ASN u 93 HIS ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 132 GLN ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 83688 Z= 0.233 Angle : 0.581 11.701 114048 Z= 0.305 Chirality : 0.042 0.306 12699 Planarity : 0.004 0.052 13884 Dihedral : 15.805 133.046 13291 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 3.39 % Allowed : 17.38 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 9398 helix: 1.77 (0.08), residues: 4161 sheet: 0.09 (0.13), residues: 1378 loop : -0.13 (0.10), residues: 3859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP m 249 HIS 0.011 0.001 HIS d 106 PHE 0.026 0.001 PHE n 262 TYR 0.037 0.001 TYR m 313 ARG 0.009 0.000 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2069 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1782 time to evaluate : 8.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7930 (mtt90) REVERT: A 16 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 37 TYR cc_start: 0.8782 (m-80) cc_final: 0.8122 (m-10) REVERT: A 39 GLU cc_start: 0.8430 (mp0) cc_final: 0.7799 (tp30) REVERT: A 50 GLU cc_start: 0.8138 (pp20) cc_final: 0.7842 (pp20) REVERT: A 54 ASN cc_start: 0.9103 (m110) cc_final: 0.8819 (m110) REVERT: A 72 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7949 (mp0) REVERT: A 145 LYS cc_start: 0.8011 (tptt) cc_final: 0.7292 (tptp) REVERT: A 146 MET cc_start: 0.8887 (ppp) cc_final: 0.8095 (tmm) REVERT: A 272 LYS cc_start: 0.9276 (ttmt) cc_final: 0.9012 (mttt) REVERT: A 283 ASP cc_start: 0.7869 (m-30) cc_final: 0.7450 (m-30) REVERT: A 298 GLN cc_start: 0.8627 (tp40) cc_final: 0.8053 (tp40) REVERT: A 306 ASP cc_start: 0.8247 (t0) cc_final: 0.7903 (t0) REVERT: A 418 TYR cc_start: 0.6457 (m-10) cc_final: 0.6255 (m-10) REVERT: A 421 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8498 (mtm-85) REVERT: A 454 MET cc_start: 0.8764 (mpp) cc_final: 0.8351 (mpp) REVERT: A 466 TYR cc_start: 0.8915 (m-80) cc_final: 0.8019 (m-80) REVERT: A 527 ASP cc_start: 0.7670 (p0) cc_final: 0.7360 (p0) REVERT: A 540 THR cc_start: 0.9397 (m) cc_final: 0.9172 (p) REVERT: A 548 MET cc_start: 0.8745 (mmm) cc_final: 0.8366 (mmm) REVERT: A 551 LEU cc_start: 0.9461 (mt) cc_final: 0.9116 (mt) REVERT: A 606 MET cc_start: 0.8610 (tpp) cc_final: 0.8086 (tpp) REVERT: A 712 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8543 (ttm-80) REVERT: A 728 ASP cc_start: 0.8731 (m-30) cc_final: 0.8447 (m-30) REVERT: A 770 MET cc_start: 0.8548 (tpp) cc_final: 0.8249 (tpp) REVERT: A 813 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 835 THR cc_start: 0.9563 (m) cc_final: 0.9266 (p) REVERT: A 863 ASP cc_start: 0.8902 (m-30) cc_final: 0.8568 (m-30) REVERT: A 971 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8614 (tm-30) REVERT: A 1073 SER cc_start: 0.9448 (m) cc_final: 0.8981 (p) REVERT: A 1128 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8825 (pp) REVERT: A 1207 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9213 (mmtm) REVERT: A 1211 MET cc_start: 0.7966 (mmm) cc_final: 0.7254 (mmm) REVERT: A 1217 LYS cc_start: 0.9448 (mmtt) cc_final: 0.9017 (mmmm) REVERT: A 1222 PHE cc_start: 0.7588 (m-80) cc_final: 0.7050 (m-80) REVERT: A 1284 LYS cc_start: 0.8780 (tptt) cc_final: 0.8265 (ttmm) REVERT: A 1354 GLU cc_start: 0.8436 (tp30) cc_final: 0.8225 (tp30) REVERT: A 1406 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7925 (tt0) REVERT: B 35 LEU cc_start: 0.9158 (mt) cc_final: 0.8882 (mm) REVERT: B 39 ASP cc_start: 0.8102 (m-30) cc_final: 0.7832 (m-30) REVERT: B 43 GLU cc_start: 0.7896 (tp30) cc_final: 0.7584 (tp30) REVERT: B 182 LYS cc_start: 0.9449 (mttt) cc_final: 0.9040 (mtmm) REVERT: B 233 SER cc_start: 0.9368 (m) cc_final: 0.9099 (t) REVERT: B 269 LYS cc_start: 0.8803 (mttm) cc_final: 0.8545 (mtpt) REVERT: B 270 GLN cc_start: 0.8773 (mm110) cc_final: 0.8345 (mm110) REVERT: B 312 GLU cc_start: 0.8524 (tt0) cc_final: 0.8288 (tt0) REVERT: B 343 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8682 (mm-40) REVERT: B 360 GLU cc_start: 0.8873 (pm20) cc_final: 0.8663 (pm20) REVERT: B 363 PHE cc_start: 0.8287 (m-80) cc_final: 0.7824 (m-80) REVERT: B 384 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8653 (mp0) REVERT: B 396 LYS cc_start: 0.9214 (mptt) cc_final: 0.8893 (mmtm) REVERT: B 419 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7379 (ttp80) REVERT: B 485 LEU cc_start: 0.9832 (mt) cc_final: 0.9597 (mt) REVERT: B 492 ASN cc_start: 0.9543 (t0) cc_final: 0.9188 (t0) REVERT: B 531 ASN cc_start: 0.8262 (m-40) cc_final: 0.6848 (m110) REVERT: B 550 PHE cc_start: 0.9016 (m-80) cc_final: 0.8646 (m-80) REVERT: B 595 ASP cc_start: 0.8357 (m-30) cc_final: 0.7846 (m-30) REVERT: B 611 ASP cc_start: 0.8208 (t0) cc_final: 0.7820 (t0) REVERT: B 656 GLN cc_start: 0.8625 (mt0) cc_final: 0.8316 (mt0) REVERT: B 661 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: B 691 ASP cc_start: 0.9013 (p0) cc_final: 0.8607 (p0) REVERT: B 706 ASP cc_start: 0.8999 (m-30) cc_final: 0.8746 (m-30) REVERT: B 754 SER cc_start: 0.9447 (m) cc_final: 0.9178 (m) REVERT: B 875 GLU cc_start: 0.8435 (pp20) cc_final: 0.8225 (pp20) REVERT: B 904 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7157 (ttt-90) REVERT: B 923 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8511 (tt0) REVERT: B 924 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: B 931 TYR cc_start: 0.9070 (p90) cc_final: 0.8639 (p90) REVERT: B 1020 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8096 (mtt-85) REVERT: B 1053 ASP cc_start: 0.8576 (m-30) cc_final: 0.8314 (m-30) REVERT: B 1146 PHE cc_start: 0.9144 (t80) cc_final: 0.8869 (t80) REVERT: B 1153 GLU cc_start: 0.7889 (mp0) cc_final: 0.7528 (mp0) REVERT: B 1168 LEU cc_start: 0.9371 (mt) cc_final: 0.9108 (mp) REVERT: C 152 GLU cc_start: 0.7577 (tp30) cc_final: 0.7280 (tp30) REVERT: D 38 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7640 (mp10) REVERT: D 45 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: D 138 HIS cc_start: 0.8169 (t-90) cc_final: 0.7557 (t-90) REVERT: D 144 GLN cc_start: 0.9419 (mm-40) cc_final: 0.8783 (tp-100) REVERT: D 183 ASP cc_start: 0.6476 (m-30) cc_final: 0.6181 (t0) REVERT: E 20 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: E 33 GLU cc_start: 0.8695 (tp30) cc_final: 0.8163 (tp30) REVERT: E 57 MET cc_start: 0.8923 (mtm) cc_final: 0.8348 (mpp) REVERT: E 73 ASP cc_start: 0.9174 (p0) cc_final: 0.8567 (p0) REVERT: E 83 ASP cc_start: 0.7490 (p0) cc_final: 0.6886 (m-30) REVERT: E 135 GLN cc_start: 0.8945 (tt0) cc_final: 0.8494 (tp40) REVERT: G 3 PHE cc_start: 0.8310 (m-80) cc_final: 0.7848 (m-80) REVERT: G 29 LYS cc_start: 0.8829 (ttmt) cc_final: 0.8568 (ttmt) REVERT: G 34 VAL cc_start: 0.9392 (t) cc_final: 0.9109 (p) REVERT: G 35 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7618 (mm-30) REVERT: G 73 LYS cc_start: 0.9321 (mttt) cc_final: 0.9000 (mtpt) REVERT: G 80 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8363 (ttmt) REVERT: H 41 ASP cc_start: 0.9083 (m-30) cc_final: 0.8465 (m-30) REVERT: H 56 THR cc_start: 0.8751 (m) cc_final: 0.8393 (p) REVERT: H 121 LEU cc_start: 0.9174 (mt) cc_final: 0.8672 (mm) REVERT: H 122 MET cc_start: 0.8963 (ttp) cc_final: 0.8602 (tmm) REVERT: I 13 MET cc_start: 0.8332 (ttm) cc_final: 0.7612 (tpp) REVERT: I 85 PHE cc_start: 0.8729 (p90) cc_final: 0.8385 (p90) REVERT: V 22 ARG cc_start: 0.5591 (mpt-90) cc_final: 0.5025 (ptm160) REVERT: W 227 TRP cc_start: 0.6939 (m-90) cc_final: 0.5238 (m-90) REVERT: W 529 ASP cc_start: 0.8866 (m-30) cc_final: 0.8633 (t70) REVERT: W 556 GLU cc_start: 0.8125 (tp30) cc_final: 0.7840 (tm-30) REVERT: W 578 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6630 (p0) REVERT: W 585 ASP cc_start: 0.8331 (t0) cc_final: 0.7943 (t0) REVERT: W 603 GLN cc_start: 0.9167 (tt0) cc_final: 0.8520 (tp-100) REVERT: W 638 TYR cc_start: 0.8482 (m-80) cc_final: 0.8211 (m-80) REVERT: W 641 LEU cc_start: 0.8322 (mm) cc_final: 0.7686 (mm) REVERT: W 663 THR cc_start: 0.8303 (m) cc_final: 0.8046 (t) REVERT: W 687 ARG cc_start: 0.8777 (ttp-170) cc_final: 0.8515 (ttp-110) REVERT: W 697 VAL cc_start: 0.8592 (p) cc_final: 0.8378 (m) REVERT: W 804 TRP cc_start: 0.6407 (m100) cc_final: 0.5767 (m100) REVERT: m 309 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7560 (ptp-170) REVERT: m 310 PHE cc_start: 0.8896 (m-80) cc_final: 0.8339 (m-10) REVERT: m 338 LEU cc_start: 0.8682 (mt) cc_final: 0.8241 (mt) REVERT: m 341 GLU cc_start: 0.7570 (tp30) cc_final: 0.7303 (pt0) REVERT: m 669 ASN cc_start: 0.8299 (m110) cc_final: 0.8013 (p0) REVERT: m 748 ASP cc_start: 0.8207 (t0) cc_final: 0.7402 (p0) REVERT: m 784 MET cc_start: 0.8800 (tmm) cc_final: 0.8422 (tmm) REVERT: m 796 PHE cc_start: 0.6261 (m-80) cc_final: 0.5953 (m-80) REVERT: m 807 ASP cc_start: 0.9483 (t0) cc_final: 0.9161 (m-30) REVERT: m 845 GLU cc_start: 0.8845 (tp30) cc_final: 0.8443 (pp20) REVERT: m 882 ARG cc_start: 0.8954 (ttm110) cc_final: 0.8614 (ttm110) REVERT: m 889 LYS cc_start: 0.8974 (tptm) cc_final: 0.8636 (tptt) REVERT: m 893 GLU cc_start: 0.8560 (tt0) cc_final: 0.8244 (pt0) REVERT: m 912 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7271 (pp30) REVERT: m 923 GLU cc_start: 0.9396 (mm-30) cc_final: 0.8924 (tm-30) REVERT: m 953 ILE cc_start: 0.7893 (mm) cc_final: 0.7500 (mm) REVERT: m 963 GLU cc_start: 0.7800 (tp30) cc_final: 0.7528 (tp30) REVERT: m 1136 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.7126 (mpp80) REVERT: m 1142 PHE cc_start: 0.8712 (t80) cc_final: 0.8408 (t80) REVERT: m 1152 GLN cc_start: 0.9451 (tt0) cc_final: 0.9211 (tp-100) REVERT: m 1166 MET cc_start: 0.8538 (mmm) cc_final: 0.7845 (mtp) REVERT: n 153 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6716 (pp20) REVERT: n 200 ARG cc_start: 0.7012 (ttt180) cc_final: 0.5946 (mmt90) REVERT: q 1 MET cc_start: 0.2308 (mmp) cc_final: 0.1399 (ttp) REVERT: q 338 TRP cc_start: 0.6426 (m100) cc_final: 0.5956 (m100) REVERT: q 404 GLU cc_start: 0.5036 (mp0) cc_final: 0.4699 (pm20) REVERT: q 467 LYS cc_start: 0.6346 (mtmt) cc_final: 0.5369 (tptp) REVERT: q 597 LEU cc_start: -0.0248 (OUTLIER) cc_final: -0.0524 (tp) REVERT: q 644 MET cc_start: 0.2293 (mtm) cc_final: -0.0341 (tmm) REVERT: q 720 PHE cc_start: 0.9189 (m-80) cc_final: 0.8932 (m-80) REVERT: q 777 GLU cc_start: 0.8384 (tp30) cc_final: 0.7743 (tm-30) REVERT: q 847 LYS cc_start: 0.8082 (pptt) cc_final: 0.7727 (tppt) REVERT: q 849 ARG cc_start: 0.7723 (ttt180) cc_final: 0.7491 (ttm170) REVERT: q 911 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6935 (mm-30) REVERT: r 318 ASP cc_start: 0.0571 (m-30) cc_final: 0.0071 (t0) REVERT: r 329 MET cc_start: -0.3031 (tmm) cc_final: -0.3369 (ttp) REVERT: r 373 ASP cc_start: 0.8223 (t0) cc_final: 0.7867 (t0) REVERT: r 401 SER cc_start: 0.9025 (m) cc_final: 0.8665 (p) REVERT: u 90 LEU cc_start: 0.7624 (mm) cc_final: 0.7174 (tp) REVERT: u 171 ILE cc_start: 0.4401 (mm) cc_final: 0.3885 (pt) REVERT: u 210 MET cc_start: 0.6949 (tpt) cc_final: 0.6717 (mtm) REVERT: u 265 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9071 (mm-30) REVERT: u 269 ASN cc_start: 0.9345 (m-40) cc_final: 0.9123 (m-40) REVERT: v 167 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6217 (tp30) REVERT: v 199 HIS cc_start: 0.4166 (OUTLIER) cc_final: 0.3852 (t-90) REVERT: v 200 PHE cc_start: 0.8287 (t80) cc_final: 0.8083 (t80) REVERT: v 252 PHE cc_start: 0.8778 (m-80) cc_final: 0.8349 (m-80) REVERT: x 240 GLU cc_start: 0.6938 (mm-30) cc_final: 0.5980 (mt-10) REVERT: x 246 ASN cc_start: 0.6041 (p0) cc_final: 0.5515 (t0) REVERT: x 247 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8852 (pp) REVERT: x 268 ASN cc_start: 0.7363 (t0) cc_final: 0.7118 (t0) REVERT: x 310 ASN cc_start: 0.8669 (m110) cc_final: 0.8446 (m110) REVERT: x 313 TYR cc_start: 0.8324 (t80) cc_final: 0.7789 (t80) REVERT: x 319 ASP cc_start: 0.7429 (m-30) cc_final: 0.6891 (m-30) REVERT: x 336 ASP cc_start: 0.6548 (t0) cc_final: 0.6166 (t0) REVERT: x 348 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7984 (tt0) REVERT: x 352 ASP cc_start: 0.8485 (m-30) cc_final: 0.8078 (m-30) REVERT: j 541 LYS cc_start: 0.0039 (tmtt) cc_final: -0.0686 (mmmt) REVERT: j 652 MET cc_start: -0.5145 (mmt) cc_final: -0.5431 (mpp) REVERT: j 740 MET cc_start: 0.5545 (mmt) cc_final: 0.5274 (mmt) REVERT: k 21 ARG cc_start: 0.4676 (mtt180) cc_final: 0.4194 (ptt180) REVERT: k 70 ARG cc_start: 0.1297 (mtt180) cc_final: 0.0766 (tpt170) REVERT: k 86 GLN cc_start: 0.7227 (mt0) cc_final: 0.6653 (pp30) outliers start: 287 outliers final: 223 residues processed: 1926 average time/residue: 0.7641 time to fit residues: 2512.0938 Evaluate side-chains 1907 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1671 time to evaluate : 7.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 996 CYS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 241 ARG Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 426 LEU Chi-restraints excluded: chain W residue 522 THR Chi-restraints excluded: chain W residue 541 ARG Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain W residue 598 LEU Chi-restraints excluded: chain W residue 629 LEU Chi-restraints excluded: chain W residue 647 GLN Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 294 LEU Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 542 MET Chi-restraints excluded: chain m residue 549 SER Chi-restraints excluded: chain m residue 575 ASP Chi-restraints excluded: chain m residue 598 SER Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 774 ASN Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 842 LEU Chi-restraints excluded: chain m residue 851 GLU Chi-restraints excluded: chain m residue 873 VAL Chi-restraints excluded: chain m residue 912 GLN Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 927 SER Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 1023 VAL Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 223 LEU Chi-restraints excluded: chain n residue 244 LEU Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 83 ILE Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 294 HIS Chi-restraints excluded: chain q residue 328 ASN Chi-restraints excluded: chain q residue 350 VAL Chi-restraints excluded: chain q residue 368 LEU Chi-restraints excluded: chain q residue 597 LEU Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 387 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 232 GLN Chi-restraints excluded: chain v residue 136 ASP Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 199 HIS Chi-restraints excluded: chain v residue 248 LEU Chi-restraints excluded: chain v residue 333 ILE Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 713 SER Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 875 VAL Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain k residue 53 SER Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 99 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 172 VAL Chi-restraints excluded: chain k residue 358 SER Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 312 optimal weight: 0.5980 chunk 836 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 545 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 929 optimal weight: 50.0000 chunk 771 optimal weight: 30.0000 chunk 430 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 488 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN A 480 ASN A 526 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN B 291 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN G 118 ASN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 538 ASN m 710 GLN ** m 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 819 ASN m 912 GLN ** m 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 970 HIS ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 482 ASN q 526 ASN ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 ASN j 693 GLN ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 102 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 83688 Z= 0.250 Angle : 0.588 11.161 114048 Z= 0.308 Chirality : 0.042 0.299 12699 Planarity : 0.004 0.068 13884 Dihedral : 15.781 131.551 13291 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % Rotamer: Outliers : 3.63 % Allowed : 17.94 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 9398 helix: 1.79 (0.08), residues: 4159 sheet: 0.07 (0.14), residues: 1369 loop : -0.13 (0.10), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP m 249 HIS 0.012 0.001 HIS d 106 PHE 0.021 0.001 PHE n 262 TYR 0.038 0.001 TYR m 313 ARG 0.010 0.000 ARG q 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2019 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1712 time to evaluate : 7.010 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: A 37 TYR cc_start: 0.8785 (m-80) cc_final: 0.8034 (m-80) REVERT: A 39 GLU cc_start: 0.8470 (mp0) cc_final: 0.7837 (tp30) REVERT: A 41 MET cc_start: 0.2142 (tpt) cc_final: 0.0645 (tpt) REVERT: A 50 GLU cc_start: 0.8111 (pp20) cc_final: 0.7787 (pp20) REVERT: A 54 ASN cc_start: 0.9053 (m110) cc_final: 0.8709 (m110) REVERT: A 72 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8238 (mp0) REVERT: A 145 LYS cc_start: 0.8115 (tptt) cc_final: 0.7522 (tptp) REVERT: A 146 MET cc_start: 0.8806 (ppp) cc_final: 0.8017 (tmm) REVERT: A 272 LYS cc_start: 0.9284 (ttmt) cc_final: 0.9082 (mtpt) REVERT: A 283 ASP cc_start: 0.7898 (m-30) cc_final: 0.7508 (m-30) REVERT: A 298 GLN cc_start: 0.8704 (tp40) cc_final: 0.8108 (tp40) REVERT: A 306 ASP cc_start: 0.8189 (t0) cc_final: 0.7723 (t0) REVERT: A 454 MET cc_start: 0.8722 (mpp) cc_final: 0.8344 (mpp) REVERT: A 466 TYR cc_start: 0.8924 (m-80) cc_final: 0.7955 (m-80) REVERT: A 540 THR cc_start: 0.9394 (m) cc_final: 0.9164 (p) REVERT: A 548 MET cc_start: 0.8724 (mmm) cc_final: 0.8361 (mmm) REVERT: A 551 LEU cc_start: 0.9457 (mt) cc_final: 0.9148 (mt) REVERT: A 606 MET cc_start: 0.8605 (tpp) cc_final: 0.8259 (tpp) REVERT: A 712 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8514 (ttm-80) REVERT: A 728 ASP cc_start: 0.8735 (m-30) cc_final: 0.8493 (m-30) REVERT: A 770 MET cc_start: 0.8558 (tpp) cc_final: 0.8253 (tpp) REVERT: A 813 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 835 THR cc_start: 0.9551 (m) cc_final: 0.9240 (p) REVERT: A 863 ASP cc_start: 0.8912 (m-30) cc_final: 0.8576 (m-30) REVERT: A 971 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 1073 SER cc_start: 0.9450 (m) cc_final: 0.8985 (p) REVERT: A 1081 MET cc_start: 0.8396 (ppp) cc_final: 0.8037 (ppp) REVERT: A 1128 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8822 (pp) REVERT: A 1207 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9151 (mmtm) REVERT: A 1211 MET cc_start: 0.7865 (mmm) cc_final: 0.7102 (mmm) REVERT: A 1274 ILE cc_start: 0.8825 (mm) cc_final: 0.8486 (mm) REVERT: A 1284 LYS cc_start: 0.8773 (tptt) cc_final: 0.8245 (ttmm) REVERT: A 1354 GLU cc_start: 0.8434 (tp30) cc_final: 0.8227 (tp30) REVERT: A 1406 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: A 1447 MET cc_start: 0.8971 (mmm) cc_final: 0.8395 (mmm) REVERT: B 35 LEU cc_start: 0.9146 (mt) cc_final: 0.8889 (mm) REVERT: B 39 ASP cc_start: 0.8261 (m-30) cc_final: 0.8005 (m-30) REVERT: B 43 GLU cc_start: 0.7936 (tp30) cc_final: 0.7563 (tp30) REVERT: B 89 MET cc_start: 0.7149 (tpt) cc_final: 0.6947 (tpt) REVERT: B 182 LYS cc_start: 0.9470 (mttt) cc_final: 0.9166 (mttp) REVERT: B 233 SER cc_start: 0.9351 (m) cc_final: 0.9104 (t) REVERT: B 269 LYS cc_start: 0.8817 (mttm) cc_final: 0.8549 (mtpt) REVERT: B 270 GLN cc_start: 0.8760 (mm110) cc_final: 0.8335 (mm110) REVERT: B 343 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8688 (mm-40) REVERT: B 360 GLU cc_start: 0.8909 (pm20) cc_final: 0.8687 (pm20) REVERT: B 363 PHE cc_start: 0.8297 (m-80) cc_final: 0.7831 (m-80) REVERT: B 384 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8659 (mp0) REVERT: B 396 LYS cc_start: 0.9233 (mptt) cc_final: 0.8927 (mmtm) REVERT: B 419 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7394 (ttp-170) REVERT: B 485 LEU cc_start: 0.9831 (mt) cc_final: 0.9597 (mt) REVERT: B 492 ASN cc_start: 0.9518 (t0) cc_final: 0.9210 (t0) REVERT: B 519 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7201 (tm-30) REVERT: B 531 ASN cc_start: 0.8181 (m-40) cc_final: 0.7710 (m110) REVERT: B 595 ASP cc_start: 0.8359 (m-30) cc_final: 0.7843 (m-30) REVERT: B 611 ASP cc_start: 0.8219 (t0) cc_final: 0.7813 (t0) REVERT: B 615 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8532 (mtp85) REVERT: B 656 GLN cc_start: 0.8684 (mt0) cc_final: 0.8382 (mt0) REVERT: B 661 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7163 (m-30) REVERT: B 691 ASP cc_start: 0.9032 (p0) cc_final: 0.8608 (p0) REVERT: B 706 ASP cc_start: 0.9003 (m-30) cc_final: 0.8733 (m-30) REVERT: B 736 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.6430 (m-70) REVERT: B 754 SER cc_start: 0.9427 (m) cc_final: 0.9163 (m) REVERT: B 875 GLU cc_start: 0.8515 (pp20) cc_final: 0.8314 (pp20) REVERT: B 904 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7091 (ttt-90) REVERT: B 923 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8531 (tt0) REVERT: B 924 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: B 1053 ASP cc_start: 0.8627 (m-30) cc_final: 0.8365 (m-30) REVERT: B 1146 PHE cc_start: 0.9150 (t80) cc_final: 0.8902 (t80) REVERT: B 1153 GLU cc_start: 0.7911 (mp0) cc_final: 0.7581 (mp0) REVERT: B 1168 LEU cc_start: 0.9369 (mt) cc_final: 0.9106 (mp) REVERT: B 1192 TYR cc_start: 0.9100 (m-80) cc_final: 0.8835 (m-10) REVERT: D 38 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7607 (mp10) REVERT: D 45 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: D 138 HIS cc_start: 0.8182 (t-90) cc_final: 0.7567 (t-90) REVERT: D 144 GLN cc_start: 0.9416 (mm-40) cc_final: 0.8803 (tp-100) REVERT: D 145 LEU cc_start: 0.9294 (pp) cc_final: 0.9076 (pp) REVERT: D 183 ASP cc_start: 0.6525 (m-30) cc_final: 0.6203 (t0) REVERT: E 20 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: E 24 ASP cc_start: 0.8208 (m-30) cc_final: 0.7923 (m-30) REVERT: E 33 GLU cc_start: 0.8663 (tp30) cc_final: 0.8105 (tp30) REVERT: E 73 ASP cc_start: 0.9176 (p0) cc_final: 0.8544 (p0) REVERT: E 135 GLN cc_start: 0.8938 (tt0) cc_final: 0.8495 (tp40) REVERT: G 3 PHE cc_start: 0.8348 (m-80) cc_final: 0.7711 (m-80) REVERT: G 34 VAL cc_start: 0.9409 (t) cc_final: 0.9148 (p) REVERT: G 35 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7635 (mm-30) REVERT: G 73 LYS cc_start: 0.9288 (mttt) cc_final: 0.8844 (mtpt) REVERT: H 41 ASP cc_start: 0.9072 (m-30) cc_final: 0.8645 (m-30) REVERT: H 56 THR cc_start: 0.8734 (m) cc_final: 0.8371 (p) REVERT: H 121 LEU cc_start: 0.9190 (mt) cc_final: 0.8840 (mm) REVERT: H 122 MET cc_start: 0.8916 (ttp) cc_final: 0.8524 (tmm) REVERT: I 13 MET cc_start: 0.8378 (ttm) cc_final: 0.7677 (tpp) REVERT: I 85 PHE cc_start: 0.8710 (p90) cc_final: 0.8405 (p90) REVERT: W 227 TRP cc_start: 0.6903 (m-90) cc_final: 0.5199 (m-90) REVERT: W 529 ASP cc_start: 0.8887 (m-30) cc_final: 0.8601 (t70) REVERT: W 556 GLU cc_start: 0.8213 (tp30) cc_final: 0.7948 (tm-30) REVERT: W 578 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.6822 (p0) REVERT: W 585 ASP cc_start: 0.8314 (t0) cc_final: 0.7915 (t0) REVERT: W 603 GLN cc_start: 0.9262 (tt0) cc_final: 0.8631 (tp-100) REVERT: W 641 LEU cc_start: 0.8345 (mm) cc_final: 0.7698 (mm) REVERT: W 663 THR cc_start: 0.8298 (m) cc_final: 0.8043 (t) REVERT: W 804 TRP cc_start: 0.6441 (m100) cc_final: 0.5749 (m100) REVERT: m 309 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7731 (ptp-170) REVERT: m 310 PHE cc_start: 0.8877 (m-80) cc_final: 0.8378 (m-10) REVERT: m 338 LEU cc_start: 0.8609 (mt) cc_final: 0.8147 (mt) REVERT: m 341 GLU cc_start: 0.7565 (tp30) cc_final: 0.7307 (pt0) REVERT: m 612 GLN cc_start: 0.8063 (pp30) cc_final: 0.7770 (pp30) REVERT: m 748 ASP cc_start: 0.8231 (t0) cc_final: 0.7401 (p0) REVERT: m 797 ASP cc_start: 0.3150 (OUTLIER) cc_final: 0.2711 (p0) REVERT: m 807 ASP cc_start: 0.9472 (t0) cc_final: 0.9162 (m-30) REVERT: m 837 ASP cc_start: 0.8789 (m-30) cc_final: 0.8447 (t70) REVERT: m 845 GLU cc_start: 0.8852 (tp30) cc_final: 0.8441 (pp20) REVERT: m 889 LYS cc_start: 0.9001 (tptm) cc_final: 0.8650 (tptt) REVERT: m 893 GLU cc_start: 0.8595 (tt0) cc_final: 0.8289 (pt0) REVERT: m 917 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7993 (mm-30) REVERT: m 923 GLU cc_start: 0.9382 (mm-30) cc_final: 0.8504 (tm-30) REVERT: m 953 ILE cc_start: 0.7738 (mm) cc_final: 0.7407 (mm) REVERT: m 1142 PHE cc_start: 0.8703 (t80) cc_final: 0.8408 (t80) REVERT: m 1152 GLN cc_start: 0.9436 (tt0) cc_final: 0.9192 (tp-100) REVERT: m 1166 MET cc_start: 0.8546 (mmm) cc_final: 0.7835 (mtp) REVERT: n 153 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6651 (pp20) REVERT: n 200 ARG cc_start: 0.6905 (ttt180) cc_final: 0.5898 (mmt90) REVERT: n 269 VAL cc_start: 0.5777 (OUTLIER) cc_final: 0.5472 (p) REVERT: q 1 MET cc_start: 0.2251 (mmp) cc_final: 0.1312 (ttp) REVERT: q 338 TRP cc_start: 0.6389 (m100) cc_final: 0.5988 (m100) REVERT: q 597 LEU cc_start: -0.0283 (OUTLIER) cc_final: -0.0546 (tp) REVERT: q 644 MET cc_start: 0.2229 (mtm) cc_final: -0.0412 (tmm) REVERT: q 720 PHE cc_start: 0.9263 (m-80) cc_final: 0.8913 (m-80) REVERT: q 744 MET cc_start: 0.5349 (ppp) cc_final: 0.4675 (pmm) REVERT: q 777 GLU cc_start: 0.8384 (tp30) cc_final: 0.7774 (tm-30) REVERT: q 849 ARG cc_start: 0.7731 (ttt180) cc_final: 0.7504 (ttm170) REVERT: q 911 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6883 (mm-30) REVERT: r 318 ASP cc_start: -0.0256 (m-30) cc_final: -0.0640 (t70) REVERT: r 329 MET cc_start: -0.3034 (tmm) cc_final: -0.3396 (ttp) REVERT: r 401 SER cc_start: 0.9025 (m) cc_final: 0.8663 (p) REVERT: u 90 LEU cc_start: 0.6942 (mm) cc_final: 0.6078 (tp) REVERT: u 171 ILE cc_start: 0.4385 (mm) cc_final: 0.3860 (pt) REVERT: u 265 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9045 (mm-30) REVERT: u 269 ASN cc_start: 0.9348 (m-40) cc_final: 0.9123 (m-40) REVERT: v 63 MET cc_start: 0.4794 (mmm) cc_final: 0.2957 (mtm) REVERT: v 167 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6211 (tp30) REVERT: v 199 HIS cc_start: 0.4034 (OUTLIER) cc_final: 0.3767 (t-90) REVERT: v 200 PHE cc_start: 0.8150 (t80) cc_final: 0.7934 (t80) REVERT: v 252 PHE cc_start: 0.8820 (m-80) cc_final: 0.8403 (m-80) REVERT: x 233 LYS cc_start: 0.8176 (pttt) cc_final: 0.7800 (pttm) REVERT: x 240 GLU cc_start: 0.6946 (mm-30) cc_final: 0.5970 (mt-10) REVERT: x 246 ASN cc_start: 0.5746 (p0) cc_final: 0.4998 (t0) REVERT: x 268 ASN cc_start: 0.7368 (t0) cc_final: 0.7154 (t0) REVERT: x 310 ASN cc_start: 0.8700 (m110) cc_final: 0.8482 (m110) REVERT: x 319 ASP cc_start: 0.7681 (m-30) cc_final: 0.7222 (m-30) REVERT: x 328 TRP cc_start: 0.6440 (m-90) cc_final: 0.5412 (m-90) REVERT: x 336 ASP cc_start: 0.6803 (t0) cc_final: 0.6424 (t0) REVERT: x 338 VAL cc_start: 0.8634 (m) cc_final: 0.8421 (m) REVERT: x 348 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7867 (tt0) REVERT: x 352 ASP cc_start: 0.8452 (m-30) cc_final: 0.8036 (m-30) REVERT: j 541 LYS cc_start: 0.0052 (tmtt) cc_final: -0.0666 (mmmt) REVERT: j 586 ILE cc_start: 0.1908 (OUTLIER) cc_final: 0.1444 (tp) REVERT: j 652 MET cc_start: -0.5138 (mmt) cc_final: -0.5415 (mpp) REVERT: k 21 ARG cc_start: 0.4618 (mtt180) cc_final: 0.4128 (ptt180) REVERT: k 70 ARG cc_start: 0.1323 (mtt180) cc_final: 0.0758 (tpt170) REVERT: k 86 GLN cc_start: 0.7161 (mt0) cc_final: 0.6535 (pp30) outliers start: 307 outliers final: 246 residues processed: 1867 average time/residue: 0.7631 time to fit residues: 2435.9948 Evaluate side-chains 1928 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1667 time to evaluate : 6.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 924 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 241 ARG Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 414 VAL Chi-restraints excluded: chain W residue 426 LEU Chi-restraints excluded: chain W residue 522 THR Chi-restraints excluded: chain W residue 541 ARG Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain W residue 598 LEU Chi-restraints excluded: chain W residue 609 VAL Chi-restraints excluded: chain W residue 647 GLN Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 294 LEU Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 542 MET Chi-restraints excluded: chain m residue 549 SER Chi-restraints excluded: chain m residue 575 ASP Chi-restraints excluded: chain m residue 598 SER Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 774 ASN Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 842 LEU Chi-restraints excluded: chain m residue 851 GLU Chi-restraints excluded: chain m residue 873 VAL Chi-restraints excluded: chain m residue 880 THR Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 927 SER Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 1023 VAL Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain m residue 1210 TYR Chi-restraints excluded: chain m residue 1234 LEU Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 185 ILE Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 244 LEU Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain n residue 269 VAL Chi-restraints excluded: chain n residue 289 MET Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 83 ILE Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 232 LEU Chi-restraints excluded: chain q residue 294 HIS Chi-restraints excluded: chain q residue 328 ASN Chi-restraints excluded: chain q residue 368 LEU Chi-restraints excluded: chain q residue 597 LEU Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 387 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 144 LEU Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain v residue 136 ASP Chi-restraints excluded: chain v residue 167 GLU Chi-restraints excluded: chain v residue 199 HIS Chi-restraints excluded: chain v residue 248 LEU Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 586 ILE Chi-restraints excluded: chain j residue 713 SER Chi-restraints excluded: chain j residue 755 VAL Chi-restraints excluded: chain j residue 790 LEU Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain j residue 875 VAL Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain k residue 53 SER Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 99 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 172 VAL Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 896 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 529 optimal weight: 6.9990 chunk 679 optimal weight: 7.9990 chunk 526 optimal weight: 40.0000 chunk 782 optimal weight: 1.9990 chunk 519 optimal weight: 1.9990 chunk 926 optimal weight: 40.0000 chunk 579 optimal weight: 10.0000 chunk 564 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 359 ASN A 480 ASN A 526 GLN A 661 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN B 63 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1097 HIS ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1211 ASN E 178 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 GLN ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 554 GLN ** m 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 998 ASN ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 328 ASN q 758 HIS ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 83688 Z= 0.296 Angle : 0.607 11.378 114048 Z= 0.317 Chirality : 0.042 0.253 12699 Planarity : 0.004 0.067 13884 Dihedral : 15.787 130.086 13291 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 3.79 % Allowed : 18.58 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 9398 helix: 1.71 (0.08), residues: 4162 sheet: 0.02 (0.13), residues: 1364 loop : -0.19 (0.10), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP m 249 HIS 0.009 0.001 HIS B 508 PHE 0.021 0.002 PHE G 109 TYR 0.036 0.001 TYR m 313 ARG 0.009 0.001 ARG E 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2023 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1702 time to evaluate : 7.240 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: A 16 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8247 (mt-10) REVERT: A 39 GLU cc_start: 0.8482 (mp0) cc_final: 0.7867 (tp30) REVERT: A 41 MET cc_start: 0.1528 (tpt) cc_final: -0.0537 (tpt) REVERT: A 50 GLU cc_start: 0.8224 (pp20) cc_final: 0.7901 (pp20) REVERT: A 54 ASN cc_start: 0.9078 (m110) cc_final: 0.8809 (m-40) REVERT: A 72 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8165 (mp0) REVERT: A 145 LYS cc_start: 0.8312 (tptt) cc_final: 0.7733 (tptp) REVERT: A 146 MET cc_start: 0.8825 (ppp) cc_final: 0.8113 (tmm) REVERT: A 272 LYS cc_start: 0.9273 (ttmt) cc_final: 0.9046 (mtpt) REVERT: A 283 ASP cc_start: 0.7731 (m-30) cc_final: 0.7364 (m-30) REVERT: A 306 ASP cc_start: 0.8379 (t0) cc_final: 0.7866 (t0) REVERT: A 309 ILE cc_start: 0.9312 (mm) cc_final: 0.8952 (mm) REVERT: A 418 TYR cc_start: 0.6384 (m-10) cc_final: 0.6145 (m-10) REVERT: A 466 TYR cc_start: 0.8886 (m-80) cc_final: 0.7800 (m-80) REVERT: A 540 THR cc_start: 0.9430 (m) cc_final: 0.9180 (p) REVERT: A 548 MET cc_start: 0.8703 (mmm) cc_final: 0.8377 (mmm) REVERT: A 551 LEU cc_start: 0.9491 (mt) cc_final: 0.9169 (mt) REVERT: A 606 MET cc_start: 0.8548 (tpp) cc_final: 0.8310 (tpp) REVERT: A 712 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8328 (ttm-80) REVERT: A 728 ASP cc_start: 0.8755 (m-30) cc_final: 0.8501 (m-30) REVERT: A 769 GLN cc_start: 0.8844 (mm110) cc_final: 0.8620 (mm-40) REVERT: A 770 MET cc_start: 0.8569 (tpp) cc_final: 0.8133 (tpp) REVERT: A 813 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 835 THR cc_start: 0.9558 (m) cc_final: 0.9229 (p) REVERT: A 863 ASP cc_start: 0.8898 (m-30) cc_final: 0.8579 (m-30) REVERT: A 971 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8634 (tm-30) REVERT: A 1057 ARG cc_start: 0.8967 (ttm-80) cc_final: 0.8490 (ttm-80) REVERT: A 1073 SER cc_start: 0.9439 (m) cc_final: 0.8996 (p) REVERT: A 1081 MET cc_start: 0.8509 (ppp) cc_final: 0.8163 (ppp) REVERT: A 1207 LYS cc_start: 0.9412 (mmtt) cc_final: 0.9098 (mmtm) REVERT: A 1211 MET cc_start: 0.7736 (mmm) cc_final: 0.6895 (mmm) REVERT: A 1284 LYS cc_start: 0.8824 (tptt) cc_final: 0.8291 (ttmm) REVERT: A 1348 ARG cc_start: 0.9227 (ptm-80) cc_final: 0.8908 (ptm-80) REVERT: A 1447 MET cc_start: 0.8954 (mmm) cc_final: 0.8448 (mmm) REVERT: B 27 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 35 LEU cc_start: 0.9181 (mt) cc_final: 0.8933 (mm) REVERT: B 39 ASP cc_start: 0.8270 (m-30) cc_final: 0.8003 (m-30) REVERT: B 43 GLU cc_start: 0.7990 (tp30) cc_final: 0.7566 (tp30) REVERT: B 91 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 118 ASP cc_start: 0.8898 (m-30) cc_final: 0.8316 (m-30) REVERT: B 233 SER cc_start: 0.9373 (m) cc_final: 0.9110 (t) REVERT: B 269 LYS cc_start: 0.8861 (mttm) cc_final: 0.8601 (mtpt) REVERT: B 270 GLN cc_start: 0.8779 (mm110) cc_final: 0.8341 (mm110) REVERT: B 281 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9144 (mm) REVERT: B 343 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8720 (mm-40) REVERT: B 363 PHE cc_start: 0.8325 (m-80) cc_final: 0.7921 (m-80) REVERT: B 384 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8672 (mp0) REVERT: B 396 LYS cc_start: 0.9237 (mptt) cc_final: 0.8964 (mmtm) REVERT: B 419 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7435 (ttp-170) REVERT: B 462 GLN cc_start: 0.8822 (tp40) cc_final: 0.8536 (tp40) REVERT: B 485 LEU cc_start: 0.9815 (mt) cc_final: 0.9601 (mt) REVERT: B 492 ASN cc_start: 0.9511 (t0) cc_final: 0.9218 (t0) REVERT: B 519 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7109 (tm-30) REVERT: B 531 ASN cc_start: 0.8167 (m-40) cc_final: 0.7200 (m110) REVERT: B 556 MET cc_start: 0.9244 (tmm) cc_final: 0.8717 (tmm) REVERT: B 595 ASP cc_start: 0.8236 (m-30) cc_final: 0.7708 (m-30) REVERT: B 611 ASP cc_start: 0.8258 (t0) cc_final: 0.7851 (t0) REVERT: B 615 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8484 (mtp85) REVERT: B 656 GLN cc_start: 0.8599 (mt0) cc_final: 0.8342 (mt0) REVERT: B 661 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: B 691 ASP cc_start: 0.9063 (p0) cc_final: 0.8608 (p0) REVERT: B 736 HIS cc_start: 0.6658 (OUTLIER) cc_final: 0.6430 (m-70) REVERT: B 754 SER cc_start: 0.9426 (m) cc_final: 0.9164 (m) REVERT: B 872 GLU cc_start: 0.8317 (mp0) cc_final: 0.7472 (mp0) REVERT: B 904 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7089 (ttt-90) REVERT: B 1134 GLU cc_start: 0.9032 (mp0) cc_final: 0.8794 (mp0) REVERT: B 1153 GLU cc_start: 0.8018 (mp0) cc_final: 0.7736 (mp0) REVERT: C 15 ASP cc_start: 0.8814 (p0) cc_final: 0.8341 (p0) REVERT: C 79 MET cc_start: 0.7814 (tpp) cc_final: 0.7588 (tpp) REVERT: C 242 GLN cc_start: 0.8763 (mt0) cc_final: 0.8473 (mt0) REVERT: D 38 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7527 (mp10) REVERT: D 45 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: D 93 THR cc_start: 0.8498 (t) cc_final: 0.8263 (t) REVERT: D 138 HIS cc_start: 0.8219 (t-90) cc_final: 0.7654 (t-90) REVERT: D 144 GLN cc_start: 0.9415 (mm-40) cc_final: 0.8808 (tp-100) REVERT: D 145 LEU cc_start: 0.9330 (pp) cc_final: 0.9126 (pp) REVERT: D 183 ASP cc_start: 0.6591 (m-30) cc_final: 0.6235 (t0) REVERT: E 20 GLU cc_start: 0.8236 (mp0) cc_final: 0.7856 (mp0) REVERT: E 24 ASP cc_start: 0.8271 (m-30) cc_final: 0.7996 (m-30) REVERT: E 33 GLU cc_start: 0.8670 (tp30) cc_final: 0.8296 (tp30) REVERT: E 54 ARG cc_start: 0.9123 (mmt90) cc_final: 0.8335 (mmt90) REVERT: E 57 MET cc_start: 0.8924 (mtm) cc_final: 0.8633 (mtm) REVERT: E 73 ASP cc_start: 0.9158 (p0) cc_final: 0.8588 (p0) REVERT: E 122 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6686 (tmm) REVERT: E 135 GLN cc_start: 0.8958 (tt0) cc_final: 0.8500 (tp40) REVERT: G 3 PHE cc_start: 0.8165 (m-80) cc_final: 0.7708 (m-80) REVERT: G 5 LYS cc_start: 0.9384 (mtpp) cc_final: 0.9042 (mtpp) REVERT: G 34 VAL cc_start: 0.9416 (t) cc_final: 0.9136 (p) REVERT: G 35 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7625 (mm-30) REVERT: G 73 LYS cc_start: 0.9292 (mttt) cc_final: 0.8840 (mtpt) REVERT: G 83 LYS cc_start: 0.8268 (tmmt) cc_final: 0.7875 (tttp) REVERT: H 41 ASP cc_start: 0.9031 (m-30) cc_final: 0.8626 (m-30) REVERT: H 56 THR cc_start: 0.8765 (m) cc_final: 0.8423 (p) REVERT: H 121 LEU cc_start: 0.9189 (mt) cc_final: 0.8838 (mm) REVERT: H 122 MET cc_start: 0.8914 (ttp) cc_final: 0.8547 (tmm) REVERT: I 13 MET cc_start: 0.8467 (ttm) cc_final: 0.7778 (tpp) REVERT: K 16 VAL cc_start: 0.9601 (t) cc_final: 0.9369 (m) REVERT: V 9 GLU cc_start: 0.6449 (tp30) cc_final: 0.6210 (tp30) REVERT: W 227 TRP cc_start: 0.7155 (m-90) cc_final: 0.5576 (m-90) REVERT: W 529 ASP cc_start: 0.8810 (m-30) cc_final: 0.8471 (t70) REVERT: W 556 GLU cc_start: 0.8284 (tp30) cc_final: 0.8003 (tm-30) REVERT: W 585 ASP cc_start: 0.8317 (t0) cc_final: 0.7925 (t0) REVERT: W 603 GLN cc_start: 0.9250 (tt0) cc_final: 0.8739 (tp-100) REVERT: W 641 LEU cc_start: 0.8422 (mm) cc_final: 0.7771 (mm) REVERT: W 804 TRP cc_start: 0.6491 (m100) cc_final: 0.5829 (m100) REVERT: m 309 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7771 (ptp-170) REVERT: m 310 PHE cc_start: 0.8968 (m-80) cc_final: 0.8465 (m-10) REVERT: m 338 LEU cc_start: 0.8769 (mt) cc_final: 0.8370 (mt) REVERT: m 341 GLU cc_start: 0.7555 (tp30) cc_final: 0.7290 (pt0) REVERT: m 612 GLN cc_start: 0.8022 (pp30) cc_final: 0.7700 (pp30) REVERT: m 797 ASP cc_start: 0.2994 (OUTLIER) cc_final: 0.2563 (p0) REVERT: m 807 ASP cc_start: 0.9502 (t0) cc_final: 0.9233 (m-30) REVERT: m 837 ASP cc_start: 0.8784 (m-30) cc_final: 0.8401 (t70) REVERT: m 845 GLU cc_start: 0.8872 (tp30) cc_final: 0.8470 (pp20) REVERT: m 846 GLU cc_start: 0.9030 (tp30) cc_final: 0.8766 (tm-30) REVERT: m 889 LYS cc_start: 0.9020 (tptm) cc_final: 0.8662 (tptt) REVERT: m 893 GLU cc_start: 0.8560 (tt0) cc_final: 0.8253 (pt0) REVERT: m 917 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7922 (mm-30) REVERT: m 953 ILE cc_start: 0.7840 (mm) cc_final: 0.7545 (mm) REVERT: m 1117 GLN cc_start: 0.7662 (mt0) cc_final: 0.7373 (mm-40) REVERT: m 1152 GLN cc_start: 0.9404 (tt0) cc_final: 0.9148 (tp-100) REVERT: n 153 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6702 (pp20) REVERT: n 200 ARG cc_start: 0.6928 (ttt180) cc_final: 0.5873 (mmt90) REVERT: n 274 LYS cc_start: 0.6689 (mmtm) cc_final: 0.6332 (mmmt) REVERT: q 1 MET cc_start: 0.2270 (mmp) cc_final: 0.1320 (ttp) REVERT: q 338 TRP cc_start: 0.6375 (m100) cc_final: 0.6123 (m100) REVERT: q 404 GLU cc_start: 0.4607 (mp0) cc_final: 0.4342 (pm20) REVERT: q 597 LEU cc_start: -0.1471 (OUTLIER) cc_final: -0.1714 (tp) REVERT: q 644 MET cc_start: 0.1837 (mtm) cc_final: 0.0169 (ttm) REVERT: q 744 MET cc_start: 0.5643 (ppp) cc_final: 0.4993 (pmm) REVERT: q 849 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7362 (ttm170) REVERT: q 911 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6838 (mm-30) REVERT: r 318 ASP cc_start: 0.0241 (m-30) cc_final: -0.0258 (t70) REVERT: r 329 MET cc_start: -0.3117 (tmm) cc_final: -0.3343 (ttp) REVERT: r 401 SER cc_start: 0.8887 (m) cc_final: 0.8548 (p) REVERT: u 247 TYR cc_start: 0.8520 (m-10) cc_final: 0.8235 (m-10) REVERT: u 265 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9051 (mm-30) REVERT: u 269 ASN cc_start: 0.9356 (m-40) cc_final: 0.8992 (m-40) REVERT: v 53 LEU cc_start: 0.5589 (tp) cc_final: 0.5331 (tt) REVERT: v 199 HIS cc_start: 0.4528 (OUTLIER) cc_final: 0.4237 (t-90) REVERT: v 252 PHE cc_start: 0.8838 (m-80) cc_final: 0.8426 (m-80) REVERT: x 233 LYS cc_start: 0.8096 (pttt) cc_final: 0.7714 (pttm) REVERT: x 246 ASN cc_start: 0.6659 (p0) cc_final: 0.6122 (t0) REVERT: x 303 GLN cc_start: 0.8983 (mp-120) cc_final: 0.8771 (mp10) REVERT: x 319 ASP cc_start: 0.7712 (m-30) cc_final: 0.7197 (m-30) REVERT: x 328 TRP cc_start: 0.6636 (m-10) cc_final: 0.6060 (m-90) REVERT: x 336 ASP cc_start: 0.6702 (t0) cc_final: 0.6389 (t0) REVERT: x 348 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7937 (tt0) REVERT: x 352 ASP cc_start: 0.8460 (m-30) cc_final: 0.8024 (m-30) REVERT: j 541 LYS cc_start: 0.0170 (tmtt) cc_final: -0.0590 (mmmt) REVERT: j 586 ILE cc_start: 0.2020 (OUTLIER) cc_final: 0.1375 (tt) REVERT: j 595 MET cc_start: 0.0306 (OUTLIER) cc_final: 0.0054 (mpp) REVERT: j 652 MET cc_start: -0.5712 (mmt) cc_final: -0.5949 (mpp) REVERT: k 21 ARG cc_start: 0.4408 (mtt180) cc_final: 0.3902 (ptt180) REVERT: k 86 GLN cc_start: 0.7208 (mt0) cc_final: 0.6576 (pp30) outliers start: 321 outliers final: 275 residues processed: 1868 average time/residue: 0.7738 time to fit residues: 2478.3442 Evaluate side-chains 1930 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1644 time to evaluate : 7.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 300 HIS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 614 MET Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1353 LYS Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 241 ARG Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 414 VAL Chi-restraints excluded: chain W residue 426 LEU Chi-restraints excluded: chain W residue 488 ASN Chi-restraints excluded: chain W residue 541 ARG Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain W residue 598 LEU Chi-restraints excluded: chain W residue 609 VAL Chi-restraints excluded: chain W residue 613 ILE Chi-restraints excluded: chain W residue 647 GLN Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 294 LEU Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 390 ASP Chi-restraints excluded: chain m residue 461 SER Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 542 MET Chi-restraints excluded: chain m residue 549 SER Chi-restraints excluded: chain m residue 553 HIS Chi-restraints excluded: chain m residue 575 ASP Chi-restraints excluded: chain m residue 650 THR Chi-restraints excluded: chain m residue 655 LEU Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 774 ASN Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 842 LEU Chi-restraints excluded: chain m residue 851 GLU Chi-restraints excluded: chain m residue 873 VAL Chi-restraints excluded: chain m residue 880 THR Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 927 SER Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 1023 VAL Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain m residue 1122 SER Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 185 ILE Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 223 LEU Chi-restraints excluded: chain n residue 244 LEU Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 83 ILE Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 232 LEU Chi-restraints excluded: chain q residue 294 HIS Chi-restraints excluded: chain q residue 350 VAL Chi-restraints excluded: chain q residue 368 LEU Chi-restraints excluded: chain q residue 597 LEU Chi-restraints excluded: chain q residue 631 LEU Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain q residue 878 LYS Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 387 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain v residue 136 ASP Chi-restraints excluded: chain v residue 199 HIS Chi-restraints excluded: chain v residue 248 LEU Chi-restraints excluded: chain v residue 257 ILE Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 586 ILE Chi-restraints excluded: chain j residue 595 MET Chi-restraints excluded: chain j residue 713 SER Chi-restraints excluded: chain j residue 720 PHE Chi-restraints excluded: chain j residue 755 VAL Chi-restraints excluded: chain j residue 790 LEU Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain j residue 913 VAL Chi-restraints excluded: chain k residue 53 SER Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 99 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 172 VAL Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 573 optimal weight: 8.9990 chunk 369 optimal weight: 3.9990 chunk 553 optimal weight: 0.9990 chunk 279 optimal weight: 0.0670 chunk 182 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 588 optimal weight: 40.0000 chunk 631 optimal weight: 50.0000 chunk 457 optimal weight: 30.0000 chunk 86 optimal weight: 3.9990 chunk 728 optimal weight: 4.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 300 HIS A 359 ASN A 480 ASN A 526 GLN A 737 ASN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS E 31 GLN E 178 GLN F 127 GLN ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 599 HIS W 648 GLN m 353 HIS ** m 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 970 HIS ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 210 ASN ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 250 ASN ** q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 363 GLN ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 148 ASN ** u 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 ASN ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 83688 Z= 0.233 Angle : 0.599 12.069 114048 Z= 0.311 Chirality : 0.042 0.256 12699 Planarity : 0.004 0.053 13884 Dihedral : 15.753 129.411 13291 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % Rotamer: Outliers : 3.39 % Allowed : 19.46 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.09), residues: 9398 helix: 1.76 (0.08), residues: 4156 sheet: 0.06 (0.14), residues: 1378 loop : -0.17 (0.10), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP u 173 HIS 0.022 0.001 HIS A 300 PHE 0.028 0.001 PHE v 200 TYR 0.038 0.001 TYR m 313 ARG 0.016 0.000 ARG m 882 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1998 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1711 time to evaluate : 7.016 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: A 16 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8187 (mt-10) REVERT: A 39 GLU cc_start: 0.8440 (mp0) cc_final: 0.7851 (tp30) REVERT: A 41 MET cc_start: 0.1395 (tpt) cc_final: -0.0612 (tpt) REVERT: A 50 GLU cc_start: 0.8153 (pp20) cc_final: 0.7830 (pp20) REVERT: A 54 ASN cc_start: 0.9074 (m110) cc_final: 0.8719 (m110) REVERT: A 145 LYS cc_start: 0.8370 (tptt) cc_final: 0.8045 (tptp) REVERT: A 283 ASP cc_start: 0.7715 (m-30) cc_final: 0.7439 (m-30) REVERT: A 306 ASP cc_start: 0.8267 (t0) cc_final: 0.7754 (t0) REVERT: A 309 ILE cc_start: 0.9295 (mm) cc_final: 0.8902 (mm) REVERT: A 415 ASP cc_start: 0.8658 (t0) cc_final: 0.8413 (t70) REVERT: A 466 TYR cc_start: 0.8919 (m-80) cc_final: 0.7963 (m-80) REVERT: A 527 ASP cc_start: 0.7749 (p0) cc_final: 0.7549 (p0) REVERT: A 535 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8565 (ttp) REVERT: A 540 THR cc_start: 0.9414 (m) cc_final: 0.9169 (p) REVERT: A 548 MET cc_start: 0.8717 (mmm) cc_final: 0.8350 (mmm) REVERT: A 551 LEU cc_start: 0.9448 (mt) cc_final: 0.9041 (mt) REVERT: A 606 MET cc_start: 0.8596 (tpp) cc_final: 0.8353 (tpp) REVERT: A 709 MET cc_start: 0.8226 (ttm) cc_final: 0.7959 (ttm) REVERT: A 712 ARG cc_start: 0.8666 (ttm110) cc_final: 0.8349 (ttm-80) REVERT: A 728 ASP cc_start: 0.8708 (m-30) cc_final: 0.8479 (m-30) REVERT: A 770 MET cc_start: 0.8563 (tpp) cc_final: 0.8108 (tpp) REVERT: A 813 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 835 THR cc_start: 0.9539 (m) cc_final: 0.9212 (p) REVERT: A 863 ASP cc_start: 0.8920 (m-30) cc_final: 0.8613 (m-30) REVERT: A 971 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8640 (tm-30) REVERT: A 1057 ARG cc_start: 0.8937 (ttm-80) cc_final: 0.8460 (ttm-80) REVERT: A 1073 SER cc_start: 0.9430 (m) cc_final: 0.8977 (p) REVERT: A 1081 MET cc_start: 0.8611 (ppp) cc_final: 0.8377 (ppp) REVERT: A 1098 LEU cc_start: 0.9005 (mt) cc_final: 0.8669 (pt) REVERT: A 1128 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8806 (pp) REVERT: A 1153 GLU cc_start: 0.8133 (mp0) cc_final: 0.7704 (mp0) REVERT: A 1207 LYS cc_start: 0.9371 (mmtt) cc_final: 0.9070 (mmtm) REVERT: A 1211 MET cc_start: 0.7666 (mmm) cc_final: 0.6909 (mmm) REVERT: A 1284 LYS cc_start: 0.8809 (tptt) cc_final: 0.8260 (ttmm) REVERT: A 1447 MET cc_start: 0.9020 (mmm) cc_final: 0.8529 (mmm) REVERT: A 1453 LEU cc_start: 0.9360 (tp) cc_final: 0.9123 (tp) REVERT: B 27 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 35 LEU cc_start: 0.9145 (mt) cc_final: 0.8887 (mm) REVERT: B 39 ASP cc_start: 0.8195 (m-30) cc_final: 0.7943 (m-30) REVERT: B 43 GLU cc_start: 0.7995 (tp30) cc_final: 0.7526 (tp30) REVERT: B 233 SER cc_start: 0.9367 (m) cc_final: 0.9117 (t) REVERT: B 281 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9138 (mm) REVERT: B 343 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8712 (mm-40) REVERT: B 360 GLU cc_start: 0.8802 (pm20) cc_final: 0.8302 (pm20) REVERT: B 363 PHE cc_start: 0.8160 (m-80) cc_final: 0.7373 (m-80) REVERT: B 384 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8666 (mp0) REVERT: B 396 LYS cc_start: 0.9254 (mptt) cc_final: 0.8966 (mmtm) REVERT: B 419 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7435 (ttp-170) REVERT: B 462 GLN cc_start: 0.8755 (tp40) cc_final: 0.8469 (tp40) REVERT: B 485 LEU cc_start: 0.9834 (mt) cc_final: 0.9593 (mt) REVERT: B 492 ASN cc_start: 0.9503 (t0) cc_final: 0.9222 (t0) REVERT: B 519 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7273 (tm-30) REVERT: B 531 ASN cc_start: 0.8205 (m-40) cc_final: 0.7814 (m110) REVERT: B 595 ASP cc_start: 0.8331 (m-30) cc_final: 0.7864 (m-30) REVERT: B 611 ASP cc_start: 0.8248 (t0) cc_final: 0.7824 (t0) REVERT: B 656 GLN cc_start: 0.8606 (mt0) cc_final: 0.8364 (mt0) REVERT: B 661 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: B 706 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8702 (m-30) REVERT: B 736 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.6439 (m-70) REVERT: B 754 SER cc_start: 0.9422 (m) cc_final: 0.9147 (m) REVERT: B 836 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 841 MET cc_start: 0.8169 (ttm) cc_final: 0.7694 (ttm) REVERT: B 904 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7053 (ttt-90) REVERT: B 923 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8494 (tt0) REVERT: B 1102 LYS cc_start: 0.9314 (mttm) cc_final: 0.9071 (mttp) REVERT: B 1153 GLU cc_start: 0.7981 (mp0) cc_final: 0.7702 (mp0) REVERT: B 1168 LEU cc_start: 0.9284 (mt) cc_final: 0.8998 (mp) REVERT: C 15 ASP cc_start: 0.8813 (p0) cc_final: 0.8351 (p0) REVERT: C 47 LEU cc_start: 0.9086 (mm) cc_final: 0.8878 (tp) REVERT: C 49 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7660 (mm-30) REVERT: D 38 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7467 (mp10) REVERT: D 45 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: D 93 THR cc_start: 0.8427 (t) cc_final: 0.8201 (t) REVERT: D 138 HIS cc_start: 0.8203 (t-90) cc_final: 0.7659 (t-90) REVERT: D 144 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8805 (tp-100) REVERT: D 145 LEU cc_start: 0.9410 (pp) cc_final: 0.9208 (pp) REVERT: D 183 ASP cc_start: 0.6575 (m-30) cc_final: 0.6190 (t0) REVERT: E 20 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: E 24 ASP cc_start: 0.8221 (m-30) cc_final: 0.7896 (m-30) REVERT: E 33 GLU cc_start: 0.8666 (tp30) cc_final: 0.8279 (tp30) REVERT: E 54 ARG cc_start: 0.9077 (mmt90) cc_final: 0.8277 (mmt90) REVERT: E 57 MET cc_start: 0.8931 (mtm) cc_final: 0.8668 (mtm) REVERT: E 73 ASP cc_start: 0.9163 (p0) cc_final: 0.8618 (p0) REVERT: E 122 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6476 (tmm) REVERT: E 135 GLN cc_start: 0.8929 (tt0) cc_final: 0.8447 (tp40) REVERT: G 5 LYS cc_start: 0.9352 (mtpp) cc_final: 0.8990 (mtpp) REVERT: G 34 VAL cc_start: 0.9389 (t) cc_final: 0.9118 (p) REVERT: G 35 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7617 (mm-30) REVERT: G 73 LYS cc_start: 0.9311 (mttt) cc_final: 0.8844 (mtpt) REVERT: G 83 LYS cc_start: 0.8250 (tmmt) cc_final: 0.7880 (tttp) REVERT: H 41 ASP cc_start: 0.8990 (m-30) cc_final: 0.8590 (m-30) REVERT: H 56 THR cc_start: 0.8709 (m) cc_final: 0.8400 (p) REVERT: H 121 LEU cc_start: 0.9179 (mt) cc_final: 0.8838 (mm) REVERT: H 122 MET cc_start: 0.8895 (ttp) cc_final: 0.8509 (tmm) REVERT: I 13 MET cc_start: 0.8473 (ttm) cc_final: 0.7782 (tpp) REVERT: I 85 PHE cc_start: 0.8735 (p90) cc_final: 0.8318 (p90) REVERT: I 87 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6204 (tp-100) REVERT: I 99 LEU cc_start: 0.7643 (mm) cc_final: 0.7372 (mm) REVERT: K 16 VAL cc_start: 0.9588 (t) cc_final: 0.9313 (m) REVERT: V 9 GLU cc_start: 0.6339 (tp30) cc_final: 0.5885 (tp30) REVERT: W 227 TRP cc_start: 0.7116 (m-90) cc_final: 0.5548 (m-90) REVERT: W 529 ASP cc_start: 0.8804 (m-30) cc_final: 0.8451 (t70) REVERT: W 556 GLU cc_start: 0.8204 (tp30) cc_final: 0.7941 (tm-30) REVERT: W 578 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.6753 (p0) REVERT: W 603 GLN cc_start: 0.9265 (tt0) cc_final: 0.8688 (tp-100) REVERT: W 638 TYR cc_start: 0.8825 (t80) cc_final: 0.8602 (t80) REVERT: W 641 LEU cc_start: 0.8446 (mm) cc_final: 0.7819 (mm) REVERT: W 804 TRP cc_start: 0.6499 (m100) cc_final: 0.5815 (m100) REVERT: m 309 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8003 (mpt-90) REVERT: m 310 PHE cc_start: 0.8933 (m-80) cc_final: 0.8587 (m-10) REVERT: m 338 LEU cc_start: 0.8769 (mt) cc_final: 0.8346 (mt) REVERT: m 341 GLU cc_start: 0.7534 (tp30) cc_final: 0.7121 (pt0) REVERT: m 386 ASN cc_start: 0.8825 (m-40) cc_final: 0.8508 (p0) REVERT: m 612 GLN cc_start: 0.8034 (pp30) cc_final: 0.7696 (pp30) REVERT: m 796 PHE cc_start: 0.6002 (m-80) cc_final: 0.5743 (m-80) REVERT: m 797 ASP cc_start: 0.2921 (OUTLIER) cc_final: 0.2561 (p0) REVERT: m 807 ASP cc_start: 0.9498 (t0) cc_final: 0.9214 (m-30) REVERT: m 837 ASP cc_start: 0.8779 (m-30) cc_final: 0.8395 (t70) REVERT: m 846 GLU cc_start: 0.9039 (tp30) cc_final: 0.8754 (tm-30) REVERT: m 884 TYR cc_start: 0.8362 (t80) cc_final: 0.7686 (t80) REVERT: m 889 LYS cc_start: 0.9041 (tptm) cc_final: 0.8690 (tptt) REVERT: m 893 GLU cc_start: 0.8529 (tt0) cc_final: 0.8241 (pt0) REVERT: m 923 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8370 (tm-30) REVERT: m 953 ILE cc_start: 0.7709 (mm) cc_final: 0.7439 (mm) REVERT: m 1058 MET cc_start: 0.7064 (mmm) cc_final: 0.6606 (mmm) REVERT: m 1117 GLN cc_start: 0.7511 (mt0) cc_final: 0.7209 (mm-40) REVERT: m 1152 GLN cc_start: 0.9404 (tt0) cc_final: 0.9144 (tp-100) REVERT: m 1166 MET cc_start: 0.8357 (mmm) cc_final: 0.7192 (mtp) REVERT: n 153 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6744 (pp20) REVERT: n 200 ARG cc_start: 0.7064 (ttt180) cc_final: 0.5996 (mmt90) REVERT: n 260 MET cc_start: 0.8682 (mmt) cc_final: 0.8473 (mtp) REVERT: q 338 TRP cc_start: 0.6356 (m100) cc_final: 0.6073 (m100) REVERT: q 597 LEU cc_start: -0.1481 (OUTLIER) cc_final: -0.1747 (tp) REVERT: q 644 MET cc_start: 0.1924 (mtm) cc_final: 0.0274 (ttm) REVERT: q 744 MET cc_start: 0.5454 (ppp) cc_final: 0.4774 (pmm) REVERT: q 777 GLU cc_start: 0.8581 (tp30) cc_final: 0.8216 (mm-30) REVERT: q 797 PHE cc_start: 0.7732 (m-10) cc_final: 0.7401 (m-10) REVERT: q 849 ARG cc_start: 0.7656 (ttt180) cc_final: 0.7444 (ttm170) REVERT: q 911 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6781 (mm-30) REVERT: r 318 ASP cc_start: -0.0244 (m-30) cc_final: -0.0598 (t70) REVERT: r 329 MET cc_start: -0.3378 (tmm) cc_final: -0.3606 (ttp) REVERT: r 401 SER cc_start: 0.8859 (m) cc_final: 0.8521 (p) REVERT: u 247 TYR cc_start: 0.8526 (m-10) cc_final: 0.8245 (m-10) REVERT: u 262 ARG cc_start: 0.8690 (ptp90) cc_final: 0.8350 (ptt90) REVERT: u 265 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9057 (mm-30) REVERT: u 269 ASN cc_start: 0.9166 (m-40) cc_final: 0.8965 (m-40) REVERT: v 189 ARG cc_start: 0.7912 (tpm170) cc_final: 0.7428 (tpp80) REVERT: v 199 HIS cc_start: 0.4557 (OUTLIER) cc_final: 0.4245 (t-90) REVERT: v 252 PHE cc_start: 0.8841 (m-80) cc_final: 0.8438 (m-80) REVERT: x 233 LYS cc_start: 0.8157 (pttt) cc_final: 0.7840 (pttm) REVERT: x 246 ASN cc_start: 0.7206 (p0) cc_final: 0.6385 (t0) REVERT: x 256 ARG cc_start: 0.6693 (mpt180) cc_final: 0.6472 (mpt180) REVERT: x 303 GLN cc_start: 0.8970 (mp-120) cc_final: 0.8733 (mp10) REVERT: x 319 ASP cc_start: 0.7733 (m-30) cc_final: 0.7213 (m-30) REVERT: x 328 TRP cc_start: 0.6436 (m-10) cc_final: 0.5761 (m-90) REVERT: x 336 ASP cc_start: 0.6698 (t0) cc_final: 0.6377 (t0) REVERT: x 348 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7870 (tt0) REVERT: x 351 TRP cc_start: 0.7753 (m100) cc_final: 0.7532 (m100) REVERT: x 352 ASP cc_start: 0.8299 (m-30) cc_final: 0.7840 (m-30) REVERT: j 541 LYS cc_start: 0.1106 (tmtt) cc_final: 0.0310 (mmmt) REVERT: k 21 ARG cc_start: 0.4406 (mtt180) cc_final: 0.3898 (ptt180) REVERT: k 70 ARG cc_start: 0.0534 (ptp-170) cc_final: -0.1042 (tpt170) REVERT: k 86 GLN cc_start: 0.7063 (mt0) cc_final: 0.6502 (pp30) outliers start: 287 outliers final: 244 residues processed: 1852 average time/residue: 0.7651 time to fit residues: 2425.0735 Evaluate side-chains 1898 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1639 time to evaluate : 7.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1353 LYS Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 805 LYS Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 414 VAL Chi-restraints excluded: chain W residue 426 LEU Chi-restraints excluded: chain W residue 541 ARG Chi-restraints excluded: chain W residue 543 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain W residue 598 LEU Chi-restraints excluded: chain W residue 609 VAL Chi-restraints excluded: chain W residue 613 ILE Chi-restraints excluded: chain W residue 647 GLN Chi-restraints excluded: chain W residue 648 GLN Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 294 LEU Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 461 SER Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 549 SER Chi-restraints excluded: chain m residue 553 HIS Chi-restraints excluded: chain m residue 575 ASP Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 774 ASN Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 880 THR Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 970 HIS Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 185 ILE Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain n residue 289 MET Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 83 ILE Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 294 HIS Chi-restraints excluded: chain q residue 350 VAL Chi-restraints excluded: chain q residue 368 LEU Chi-restraints excluded: chain q residue 597 LEU Chi-restraints excluded: chain q residue 631 LEU Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 387 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain v residue 136 ASP Chi-restraints excluded: chain v residue 199 HIS Chi-restraints excluded: chain v residue 248 LEU Chi-restraints excluded: chain v residue 257 ILE Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 153 ASN Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 338 VAL Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 713 SER Chi-restraints excluded: chain j residue 720 PHE Chi-restraints excluded: chain j residue 755 VAL Chi-restraints excluded: chain j residue 790 LEU Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain j residue 913 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 172 VAL Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 842 optimal weight: 30.0000 chunk 887 optimal weight: 30.0000 chunk 809 optimal weight: 10.0000 chunk 863 optimal weight: 20.0000 chunk 519 optimal weight: 3.9990 chunk 376 optimal weight: 3.9990 chunk 677 optimal weight: 40.0000 chunk 264 optimal weight: 4.9990 chunk 779 optimal weight: 10.0000 chunk 816 optimal weight: 0.6980 chunk 860 optimal weight: 50.0000 overall best weight: 4.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 480 ASN A 504 GLN A 526 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN E 178 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 512 HIS ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 599 HIS ** m 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 970 HIS ** n 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 615 HIS ** q 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 266 ASN u 169 GLN ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 83688 Z= 0.342 Angle : 0.650 11.885 114048 Z= 0.338 Chirality : 0.043 0.282 12699 Planarity : 0.004 0.085 13884 Dihedral : 15.789 128.740 13291 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 3.66 % Allowed : 19.50 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.09), residues: 9398 helix: 1.61 (0.08), residues: 4179 sheet: -0.04 (0.14), residues: 1327 loop : -0.24 (0.10), residues: 3892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP u 106 HIS 0.022 0.001 HIS m 970 PHE 0.026 0.002 PHE G 109 TYR 0.047 0.002 TYR j 929 ARG 0.016 0.001 ARG m 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1949 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1639 time to evaluate : 8.060 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: A 16 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 39 GLU cc_start: 0.8514 (mp0) cc_final: 0.7889 (tp30) REVERT: A 41 MET cc_start: 0.1455 (tpt) cc_final: -0.0540 (tpt) REVERT: A 50 GLU cc_start: 0.8195 (pp20) cc_final: 0.7902 (pp20) REVERT: A 54 ASN cc_start: 0.9105 (m110) cc_final: 0.8826 (m-40) REVERT: A 145 LYS cc_start: 0.8240 (tptt) cc_final: 0.7968 (tptp) REVERT: A 283 ASP cc_start: 0.7781 (m-30) cc_final: 0.7377 (m-30) REVERT: A 306 ASP cc_start: 0.8414 (t0) cc_final: 0.7872 (t0) REVERT: A 309 ILE cc_start: 0.9304 (mm) cc_final: 0.9009 (mm) REVERT: A 415 ASP cc_start: 0.8747 (t0) cc_final: 0.8511 (t70) REVERT: A 466 TYR cc_start: 0.8899 (m-80) cc_final: 0.7856 (m-80) REVERT: A 467 SER cc_start: 0.9080 (m) cc_final: 0.8455 (p) REVERT: A 535 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8611 (ttp) REVERT: A 540 THR cc_start: 0.9419 (m) cc_final: 0.9157 (p) REVERT: A 548 MET cc_start: 0.8712 (mmm) cc_final: 0.8370 (mmm) REVERT: A 551 LEU cc_start: 0.9473 (mt) cc_final: 0.9148 (mt) REVERT: A 606 MET cc_start: 0.8556 (tpp) cc_final: 0.8321 (tpp) REVERT: A 712 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8312 (ttm-80) REVERT: A 728 ASP cc_start: 0.8748 (m-30) cc_final: 0.8512 (m-30) REVERT: A 770 MET cc_start: 0.8578 (tpp) cc_final: 0.8244 (tpp) REVERT: A 813 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8060 (mt-10) REVERT: A 835 THR cc_start: 0.9560 (m) cc_final: 0.9210 (p) REVERT: A 863 ASP cc_start: 0.8928 (m-30) cc_final: 0.8597 (m-30) REVERT: A 971 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8658 (tm-30) REVERT: A 1073 SER cc_start: 0.9434 (m) cc_final: 0.9007 (p) REVERT: A 1081 MET cc_start: 0.8552 (ppp) cc_final: 0.8088 (ppp) REVERT: A 1153 GLU cc_start: 0.7987 (mp0) cc_final: 0.7518 (mp0) REVERT: A 1207 LYS cc_start: 0.9373 (mmtt) cc_final: 0.9047 (mmtm) REVERT: A 1211 MET cc_start: 0.7585 (mmm) cc_final: 0.6868 (mmm) REVERT: A 1284 LYS cc_start: 0.8815 (tptt) cc_final: 0.8309 (ttmm) REVERT: A 1447 MET cc_start: 0.8900 (mmm) cc_final: 0.8348 (mmm) REVERT: B 27 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8037 (tm-30) REVERT: B 35 LEU cc_start: 0.9155 (mt) cc_final: 0.8900 (mm) REVERT: B 39 ASP cc_start: 0.8230 (m-30) cc_final: 0.7976 (m-30) REVERT: B 40 GLU cc_start: 0.8336 (tp30) cc_final: 0.8061 (tp30) REVERT: B 43 GLU cc_start: 0.8024 (tp30) cc_final: 0.7573 (tp30) REVERT: B 233 SER cc_start: 0.9377 (m) cc_final: 0.9138 (t) REVERT: B 281 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9147 (mm) REVERT: B 343 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8717 (mm-40) REVERT: B 363 PHE cc_start: 0.8092 (m-80) cc_final: 0.7825 (m-80) REVERT: B 384 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8690 (mp0) REVERT: B 396 LYS cc_start: 0.9263 (mptt) cc_final: 0.8960 (mmtm) REVERT: B 419 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7487 (ttp-170) REVERT: B 485 LEU cc_start: 0.9838 (mt) cc_final: 0.9629 (mt) REVERT: B 492 ASN cc_start: 0.9511 (t0) cc_final: 0.9220 (t0) REVERT: B 519 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7308 (tm-30) REVERT: B 531 ASN cc_start: 0.8251 (m-40) cc_final: 0.7439 (m110) REVERT: B 595 ASP cc_start: 0.8287 (m-30) cc_final: 0.7811 (m-30) REVERT: B 611 ASP cc_start: 0.8293 (t0) cc_final: 0.7860 (t0) REVERT: B 656 GLN cc_start: 0.8600 (mt0) cc_final: 0.8347 (mt0) REVERT: B 661 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 706 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8733 (m-30) REVERT: B 754 SER cc_start: 0.9390 (m) cc_final: 0.9121 (m) REVERT: B 904 ARG cc_start: 0.7361 (ttp80) cc_final: 0.7041 (ttt-90) REVERT: B 1102 LYS cc_start: 0.9346 (mttm) cc_final: 0.9083 (mttp) REVERT: B 1134 GLU cc_start: 0.9086 (mp0) cc_final: 0.8692 (mp0) REVERT: B 1153 GLU cc_start: 0.8024 (mp0) cc_final: 0.7761 (mp0) REVERT: C 15 ASP cc_start: 0.8934 (p0) cc_final: 0.8494 (p0) REVERT: C 79 MET cc_start: 0.7874 (tpp) cc_final: 0.7633 (tpp) REVERT: C 242 GLN cc_start: 0.8844 (mt0) cc_final: 0.8605 (mt0) REVERT: D 38 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7489 (mp10) REVERT: D 45 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: D 93 THR cc_start: 0.8322 (t) cc_final: 0.8095 (t) REVERT: D 138 HIS cc_start: 0.8238 (t-90) cc_final: 0.7709 (t-90) REVERT: D 144 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8779 (tp-100) REVERT: D 183 ASP cc_start: 0.6380 (m-30) cc_final: 0.5993 (t0) REVERT: E 20 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: E 24 ASP cc_start: 0.8257 (m-30) cc_final: 0.7942 (m-30) REVERT: E 33 GLU cc_start: 0.8637 (tp30) cc_final: 0.8426 (tp30) REVERT: E 54 ARG cc_start: 0.9080 (mmt90) cc_final: 0.8252 (mmt90) REVERT: E 57 MET cc_start: 0.9031 (mtm) cc_final: 0.8634 (mtm) REVERT: E 73 ASP cc_start: 0.9067 (p0) cc_final: 0.8396 (p0) REVERT: E 82 CYS cc_start: 0.6805 (t) cc_final: 0.6360 (t) REVERT: E 122 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6491 (tmm) REVERT: E 135 GLN cc_start: 0.8965 (tt0) cc_final: 0.8522 (tp40) REVERT: F 112 GLU cc_start: 0.9085 (mp0) cc_final: 0.8796 (mp0) REVERT: G 5 LYS cc_start: 0.9384 (mtpp) cc_final: 0.9065 (mtpp) REVERT: G 34 VAL cc_start: 0.9408 (t) cc_final: 0.9113 (p) REVERT: G 35 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7600 (mm-30) REVERT: G 73 LYS cc_start: 0.9308 (mttt) cc_final: 0.8860 (mtpt) REVERT: H 41 ASP cc_start: 0.8970 (m-30) cc_final: 0.8563 (m-30) REVERT: H 56 THR cc_start: 0.8761 (m) cc_final: 0.8413 (p) REVERT: H 121 LEU cc_start: 0.9174 (mt) cc_final: 0.8809 (mm) REVERT: H 122 MET cc_start: 0.8807 (ttp) cc_final: 0.8447 (tmm) REVERT: I 13 MET cc_start: 0.8450 (ttm) cc_final: 0.7721 (tpp) REVERT: I 87 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6262 (tp-100) REVERT: K 16 VAL cc_start: 0.9601 (t) cc_final: 0.9346 (m) REVERT: V 9 GLU cc_start: 0.6578 (tp30) cc_final: 0.6134 (tp30) REVERT: W 227 TRP cc_start: 0.7150 (m-90) cc_final: 0.5559 (m-90) REVERT: W 529 ASP cc_start: 0.8828 (m-30) cc_final: 0.8474 (t70) REVERT: W 578 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7055 (p0) REVERT: W 603 GLN cc_start: 0.9239 (tt0) cc_final: 0.8618 (tp40) REVERT: W 638 TYR cc_start: 0.8920 (t80) cc_final: 0.8639 (t80) REVERT: W 641 LEU cc_start: 0.8525 (mm) cc_final: 0.7917 (mm) REVERT: W 804 TRP cc_start: 0.6542 (m100) cc_final: 0.5838 (m100) REVERT: m 293 MET cc_start: 0.7887 (ttm) cc_final: 0.7451 (tmm) REVERT: m 309 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8014 (mpt-90) REVERT: m 338 LEU cc_start: 0.8847 (mt) cc_final: 0.8460 (mt) REVERT: m 341 GLU cc_start: 0.7570 (tp30) cc_final: 0.7241 (pt0) REVERT: m 612 GLN cc_start: 0.7923 (pp30) cc_final: 0.7592 (pp30) REVERT: m 676 MET cc_start: 0.1829 (pmm) cc_final: 0.1594 (pmm) REVERT: m 775 ARG cc_start: 0.7671 (tpp80) cc_final: 0.6957 (mtp180) REVERT: m 796 PHE cc_start: 0.6059 (m-80) cc_final: 0.5754 (m-80) REVERT: m 797 ASP cc_start: 0.3263 (OUTLIER) cc_final: 0.2828 (p0) REVERT: m 807 ASP cc_start: 0.9533 (t0) cc_final: 0.9275 (m-30) REVERT: m 837 ASP cc_start: 0.8770 (m-30) cc_final: 0.8397 (t70) REVERT: m 842 LEU cc_start: 0.8925 (tp) cc_final: 0.8678 (tp) REVERT: m 845 GLU cc_start: 0.8875 (tp30) cc_final: 0.8577 (pp20) REVERT: m 846 GLU cc_start: 0.9050 (tp30) cc_final: 0.8781 (tm-30) REVERT: m 884 TYR cc_start: 0.8486 (t80) cc_final: 0.7998 (t80) REVERT: m 889 LYS cc_start: 0.9027 (tptm) cc_final: 0.8668 (tptt) REVERT: m 893 GLU cc_start: 0.8531 (tt0) cc_final: 0.8178 (pt0) REVERT: m 947 GLN cc_start: 0.8544 (mp10) cc_final: 0.8318 (mp10) REVERT: m 953 ILE cc_start: 0.7818 (mm) cc_final: 0.7189 (mm) REVERT: m 1117 GLN cc_start: 0.7640 (mt0) cc_final: 0.7265 (mm-40) REVERT: m 1152 GLN cc_start: 0.9415 (tt0) cc_final: 0.9114 (tp-100) REVERT: m 1166 MET cc_start: 0.8414 (mmm) cc_final: 0.8155 (mmt) REVERT: n 153 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6503 (pp20) REVERT: n 200 ARG cc_start: 0.7086 (ttt180) cc_final: 0.6059 (mmt90) REVERT: n 260 MET cc_start: 0.8660 (mmt) cc_final: 0.8411 (mtp) REVERT: q 1 MET cc_start: 0.2367 (mmp) cc_final: 0.1429 (ttp) REVERT: q 338 TRP cc_start: 0.6341 (m100) cc_final: 0.6109 (m100) REVERT: q 404 GLU cc_start: 0.4661 (mp0) cc_final: 0.4392 (pm20) REVERT: q 597 LEU cc_start: -0.1454 (OUTLIER) cc_final: -0.1715 (tp) REVERT: q 644 MET cc_start: 0.1341 (mtm) cc_final: -0.0274 (ttm) REVERT: q 744 MET cc_start: 0.5762 (ppp) cc_final: 0.5055 (pmm) REVERT: q 849 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7361 (ttm170) REVERT: q 911 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6796 (mm-30) REVERT: r 318 ASP cc_start: -0.0193 (m-30) cc_final: -0.0518 (t70) REVERT: r 329 MET cc_start: -0.3563 (tmm) cc_final: -0.3767 (ttp) REVERT: r 383 ILE cc_start: 0.9313 (mm) cc_final: 0.9109 (pt) REVERT: r 401 SER cc_start: 0.8901 (m) cc_final: 0.8567 (p) REVERT: u 171 ILE cc_start: 0.4107 (tp) cc_final: 0.3377 (pt) REVERT: u 255 GLU cc_start: 0.8391 (pm20) cc_final: 0.8188 (pm20) REVERT: u 265 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9024 (mm-30) REVERT: u 269 ASN cc_start: 0.9212 (m-40) cc_final: 0.9000 (m-40) REVERT: v 63 MET cc_start: 0.4819 (mmm) cc_final: 0.3519 (mpp) REVERT: v 199 HIS cc_start: 0.4864 (OUTLIER) cc_final: 0.4500 (t-90) REVERT: v 252 PHE cc_start: 0.8858 (m-80) cc_final: 0.8456 (m-80) REVERT: x 233 LYS cc_start: 0.8216 (pttt) cc_final: 0.7850 (pttm) REVERT: x 240 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6033 (mt-10) REVERT: x 246 ASN cc_start: 0.7086 (p0) cc_final: 0.6439 (t0) REVERT: x 303 GLN cc_start: 0.8976 (mp-120) cc_final: 0.8741 (mp10) REVERT: x 319 ASP cc_start: 0.7706 (m-30) cc_final: 0.7158 (m-30) REVERT: x 328 TRP cc_start: 0.6622 (m-10) cc_final: 0.6160 (m-90) REVERT: x 348 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7776 (tt0) REVERT: x 351 TRP cc_start: 0.7645 (m100) cc_final: 0.7398 (m100) REVERT: x 352 ASP cc_start: 0.8305 (m-30) cc_final: 0.7864 (m-30) REVERT: j 541 LYS cc_start: 0.0865 (tmtt) cc_final: 0.0212 (mmmt) REVERT: j 652 MET cc_start: -0.2488 (mpp) cc_final: -0.3080 (ppp) REVERT: k 21 ARG cc_start: 0.3723 (mtt180) cc_final: 0.3277 (ptt180) REVERT: k 70 ARG cc_start: 0.0547 (ptp-170) cc_final: -0.1032 (tpt170) REVERT: k 86 GLN cc_start: 0.6970 (mt0) cc_final: 0.6526 (pp30) outliers start: 310 outliers final: 267 residues processed: 1802 average time/residue: 0.7636 time to fit residues: 2365.0829 Evaluate side-chains 1876 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1596 time to evaluate : 7.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1353 LYS Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1400 LEU Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1448 ILE Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 414 VAL Chi-restraints excluded: chain W residue 426 LEU Chi-restraints excluded: chain W residue 488 ASN Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain W residue 598 LEU Chi-restraints excluded: chain W residue 609 VAL Chi-restraints excluded: chain W residue 613 ILE Chi-restraints excluded: chain W residue 618 ASP Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 294 LEU Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 461 SER Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 553 HIS Chi-restraints excluded: chain m residue 575 ASP Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 774 ASN Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 880 THR Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 970 HIS Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain m residue 1234 LEU Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 185 ILE Chi-restraints excluded: chain n residue 197 ILE Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 350 VAL Chi-restraints excluded: chain q residue 368 LEU Chi-restraints excluded: chain q residue 597 LEU Chi-restraints excluded: chain q residue 631 LEU Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain q residue 878 LYS Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 387 LEU Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 232 GLN Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain v residue 136 ASP Chi-restraints excluded: chain v residue 199 HIS Chi-restraints excluded: chain v residue 210 VAL Chi-restraints excluded: chain v residue 248 LEU Chi-restraints excluded: chain v residue 257 ILE Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 333 ILE Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 153 ASN Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 316 TYR Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 321 VAL Chi-restraints excluded: chain x residue 338 VAL Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 713 SER Chi-restraints excluded: chain j residue 720 PHE Chi-restraints excluded: chain j residue 747 PHE Chi-restraints excluded: chain j residue 801 GLU Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain j residue 913 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 53 SER Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 99 ASN Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 172 VAL Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 566 optimal weight: 0.8980 chunk 912 optimal weight: 30.0000 chunk 557 optimal weight: 30.0000 chunk 432 optimal weight: 0.5980 chunk 634 optimal weight: 7.9990 chunk 957 optimal weight: 40.0000 chunk 881 optimal weight: 9.9990 chunk 762 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 588 optimal weight: 40.0000 chunk 467 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 359 ASN A 504 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS E 178 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 512 HIS ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 599 HIS ** m 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 970 HIS ** n 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 83688 Z= 0.270 Angle : 0.636 19.801 114048 Z= 0.330 Chirality : 0.043 0.315 12699 Planarity : 0.004 0.081 13884 Dihedral : 15.775 128.931 13291 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 3.37 % Allowed : 20.21 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.09), residues: 9398 helix: 1.61 (0.08), residues: 4178 sheet: -0.07 (0.14), residues: 1349 loop : -0.25 (0.10), residues: 3871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP V 67 HIS 0.020 0.001 HIS m 970 PHE 0.023 0.001 PHE v 200 TYR 0.051 0.002 TYR m 969 ARG 0.014 0.000 ARG m 882 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18796 Ramachandran restraints generated. 9398 Oldfield, 0 Emsley, 9398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1941 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1656 time to evaluate : 7.003 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: A 16 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8039 (mt-10) REVERT: A 37 TYR cc_start: 0.8885 (m-80) cc_final: 0.8200 (m-10) REVERT: A 39 GLU cc_start: 0.8495 (mp0) cc_final: 0.7878 (tp30) REVERT: A 41 MET cc_start: 0.1761 (tpt) cc_final: -0.0196 (tpt) REVERT: A 50 GLU cc_start: 0.8146 (pp20) cc_final: 0.7796 (pp20) REVERT: A 54 ASN cc_start: 0.9071 (m110) cc_final: 0.8742 (m110) REVERT: A 283 ASP cc_start: 0.7942 (m-30) cc_final: 0.7587 (m-30) REVERT: A 306 ASP cc_start: 0.8271 (t0) cc_final: 0.7709 (t0) REVERT: A 309 ILE cc_start: 0.9290 (mm) cc_final: 0.8969 (mm) REVERT: A 415 ASP cc_start: 0.8736 (t0) cc_final: 0.8487 (t70) REVERT: A 466 TYR cc_start: 0.8867 (m-80) cc_final: 0.7840 (m-80) REVERT: A 535 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8586 (ttp) REVERT: A 540 THR cc_start: 0.9393 (m) cc_final: 0.9159 (p) REVERT: A 548 MET cc_start: 0.8702 (mmm) cc_final: 0.8435 (mmm) REVERT: A 551 LEU cc_start: 0.9471 (mt) cc_final: 0.9088 (mt) REVERT: A 606 MET cc_start: 0.8569 (tpp) cc_final: 0.8307 (tpp) REVERT: A 712 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8121 (ttm-80) REVERT: A 728 ASP cc_start: 0.8697 (m-30) cc_final: 0.8484 (m-30) REVERT: A 770 MET cc_start: 0.8567 (tpp) cc_final: 0.8092 (tpp) REVERT: A 813 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 835 THR cc_start: 0.9542 (m) cc_final: 0.9206 (p) REVERT: A 863 ASP cc_start: 0.8895 (m-30) cc_final: 0.8589 (m-30) REVERT: A 971 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8652 (tm-30) REVERT: A 1073 SER cc_start: 0.9428 (m) cc_final: 0.8978 (p) REVERT: A 1081 MET cc_start: 0.8685 (ppp) cc_final: 0.8056 (ppp) REVERT: A 1153 GLU cc_start: 0.7995 (mp0) cc_final: 0.7509 (mp0) REVERT: A 1207 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8994 (mmtm) REVERT: A 1211 MET cc_start: 0.7535 (mmm) cc_final: 0.6815 (mmm) REVERT: A 1284 LYS cc_start: 0.8834 (tptt) cc_final: 0.8317 (ttmm) REVERT: A 1447 MET cc_start: 0.9004 (mmm) cc_final: 0.8517 (mmm) REVERT: A 1453 LEU cc_start: 0.9357 (tp) cc_final: 0.9143 (tp) REVERT: B 27 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 35 LEU cc_start: 0.9162 (mt) cc_final: 0.8901 (mm) REVERT: B 39 ASP cc_start: 0.8139 (m-30) cc_final: 0.7874 (m-30) REVERT: B 40 GLU cc_start: 0.8295 (tp30) cc_final: 0.8000 (tp30) REVERT: B 43 GLU cc_start: 0.8032 (tp30) cc_final: 0.7544 (tp30) REVERT: B 233 SER cc_start: 0.9364 (m) cc_final: 0.9127 (t) REVERT: B 281 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9153 (mm) REVERT: B 343 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8707 (mm-40) REVERT: B 360 GLU cc_start: 0.8807 (pm20) cc_final: 0.8333 (pm20) REVERT: B 363 PHE cc_start: 0.8111 (m-80) cc_final: 0.7452 (m-80) REVERT: B 384 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8678 (mp0) REVERT: B 396 LYS cc_start: 0.9231 (mptt) cc_final: 0.8943 (mmtm) REVERT: B 419 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7469 (ttp-170) REVERT: B 492 ASN cc_start: 0.9513 (t0) cc_final: 0.9225 (t0) REVERT: B 519 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 531 ASN cc_start: 0.8211 (m-40) cc_final: 0.7486 (m110) REVERT: B 552 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 556 MET cc_start: 0.9153 (tmm) cc_final: 0.8613 (tmm) REVERT: B 595 ASP cc_start: 0.8308 (m-30) cc_final: 0.7857 (m-30) REVERT: B 611 ASP cc_start: 0.8262 (t0) cc_final: 0.7825 (t0) REVERT: B 656 GLN cc_start: 0.8616 (mt0) cc_final: 0.8369 (mt0) REVERT: B 661 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 706 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8707 (m-30) REVERT: B 754 SER cc_start: 0.9395 (m) cc_final: 0.9119 (m) REVERT: B 923 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8336 (tt0) REVERT: B 1102 LYS cc_start: 0.9328 (mttm) cc_final: 0.9036 (mttp) REVERT: B 1152 MET cc_start: 0.8857 (tpt) cc_final: 0.8374 (tpt) REVERT: B 1153 GLU cc_start: 0.7993 (mp0) cc_final: 0.7694 (mp0) REVERT: C 15 ASP cc_start: 0.8913 (p0) cc_final: 0.8629 (p0) REVERT: C 79 MET cc_start: 0.7942 (tpp) cc_final: 0.7710 (tpp) REVERT: C 242 GLN cc_start: 0.8699 (mt0) cc_final: 0.8439 (mt0) REVERT: D 34 PHE cc_start: 0.8723 (m-80) cc_final: 0.8253 (t80) REVERT: D 38 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7438 (mp10) REVERT: D 45 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: D 93 THR cc_start: 0.8289 (t) cc_final: 0.8060 (t) REVERT: D 138 HIS cc_start: 0.8264 (t-90) cc_final: 0.7705 (t-90) REVERT: D 144 GLN cc_start: 0.9353 (mm-40) cc_final: 0.8779 (tp-100) REVERT: D 183 ASP cc_start: 0.6389 (m-30) cc_final: 0.5985 (t0) REVERT: E 20 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: E 24 ASP cc_start: 0.8226 (m-30) cc_final: 0.7882 (m-30) REVERT: E 33 GLU cc_start: 0.8653 (tp30) cc_final: 0.8438 (tp30) REVERT: E 54 ARG cc_start: 0.9050 (mmt90) cc_final: 0.8242 (mmt90) REVERT: E 57 MET cc_start: 0.8908 (mtm) cc_final: 0.8661 (mtm) REVERT: E 73 ASP cc_start: 0.9059 (p0) cc_final: 0.8460 (p0) REVERT: E 82 CYS cc_start: 0.7100 (t) cc_final: 0.6772 (t) REVERT: E 122 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6425 (tmm) REVERT: E 135 GLN cc_start: 0.8932 (tt0) cc_final: 0.8494 (tp40) REVERT: F 112 GLU cc_start: 0.8990 (mp0) cc_final: 0.8747 (mp0) REVERT: G 3 PHE cc_start: 0.8461 (m-80) cc_final: 0.8010 (m-80) REVERT: G 5 LYS cc_start: 0.9366 (mtpp) cc_final: 0.9058 (mtpp) REVERT: G 34 VAL cc_start: 0.9406 (t) cc_final: 0.9121 (p) REVERT: G 35 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7647 (mm-30) REVERT: G 73 LYS cc_start: 0.9311 (mttt) cc_final: 0.8860 (mtpt) REVERT: G 83 LYS cc_start: 0.8221 (tmmt) cc_final: 0.7803 (tttt) REVERT: H 41 ASP cc_start: 0.8995 (m-30) cc_final: 0.8618 (m-30) REVERT: H 56 THR cc_start: 0.8758 (m) cc_final: 0.8427 (p) REVERT: H 121 LEU cc_start: 0.9175 (mt) cc_final: 0.8836 (mm) REVERT: H 122 MET cc_start: 0.8897 (ttp) cc_final: 0.8522 (tmm) REVERT: I 13 MET cc_start: 0.8508 (ttm) cc_final: 0.7827 (tpp) REVERT: I 85 PHE cc_start: 0.8543 (p90) cc_final: 0.8108 (p90) REVERT: I 86 PHE cc_start: 0.6797 (p90) cc_final: 0.6547 (p90) REVERT: V 9 GLU cc_start: 0.6570 (tp30) cc_final: 0.6155 (tp30) REVERT: V 39 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7542 (ptp-170) REVERT: W 227 TRP cc_start: 0.7126 (m-90) cc_final: 0.5538 (m-90) REVERT: W 529 ASP cc_start: 0.8833 (m-30) cc_final: 0.8495 (t70) REVERT: W 578 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7054 (p0) REVERT: W 603 GLN cc_start: 0.9237 (tt0) cc_final: 0.8617 (tp40) REVERT: W 638 TYR cc_start: 0.8924 (t80) cc_final: 0.8634 (t80) REVERT: W 641 LEU cc_start: 0.8533 (mm) cc_final: 0.7920 (mm) REVERT: W 804 TRP cc_start: 0.6498 (m100) cc_final: 0.5830 (m100) REVERT: m 293 MET cc_start: 0.7822 (ttm) cc_final: 0.7371 (tmm) REVERT: m 309 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.7944 (ptp-170) REVERT: m 338 LEU cc_start: 0.8843 (mt) cc_final: 0.8440 (mt) REVERT: m 341 GLU cc_start: 0.7517 (tp30) cc_final: 0.7214 (pt0) REVERT: m 407 LYS cc_start: 0.7298 (tttp) cc_final: 0.7082 (tttm) REVERT: m 612 GLN cc_start: 0.7542 (pp30) cc_final: 0.7250 (pp30) REVERT: m 667 LEU cc_start: 0.8859 (mm) cc_final: 0.8625 (mm) REVERT: m 676 MET cc_start: 0.1918 (pmm) cc_final: 0.1611 (pmm) REVERT: m 796 PHE cc_start: 0.5955 (m-80) cc_final: 0.5687 (m-80) REVERT: m 797 ASP cc_start: 0.3005 (OUTLIER) cc_final: 0.2585 (p0) REVERT: m 807 ASP cc_start: 0.9536 (t0) cc_final: 0.9278 (m-30) REVERT: m 837 ASP cc_start: 0.8764 (m-30) cc_final: 0.8392 (t70) REVERT: m 846 GLU cc_start: 0.9059 (tp30) cc_final: 0.8772 (tm-30) REVERT: m 884 TYR cc_start: 0.8532 (t80) cc_final: 0.7793 (t80) REVERT: m 889 LYS cc_start: 0.9103 (tptm) cc_final: 0.8752 (tptt) REVERT: m 893 GLU cc_start: 0.8547 (tt0) cc_final: 0.8130 (pt0) REVERT: m 925 MET cc_start: 0.9060 (tmm) cc_final: 0.8406 (ppp) REVERT: m 947 GLN cc_start: 0.8527 (mp10) cc_final: 0.8293 (mp10) REVERT: m 953 ILE cc_start: 0.7381 (mm) cc_final: 0.7104 (mm) REVERT: m 1058 MET cc_start: 0.6818 (mmm) cc_final: 0.6314 (mmm) REVERT: m 1117 GLN cc_start: 0.7637 (mt0) cc_final: 0.7265 (mm-40) REVERT: m 1152 GLN cc_start: 0.9411 (tt0) cc_final: 0.9111 (tp-100) REVERT: m 1166 MET cc_start: 0.8448 (mmm) cc_final: 0.8181 (mmt) REVERT: n 200 ARG cc_start: 0.6910 (ttt180) cc_final: 0.5892 (mmt90) REVERT: n 260 MET cc_start: 0.8675 (mmt) cc_final: 0.8423 (tmm) REVERT: q 1 MET cc_start: 0.2325 (mmp) cc_final: 0.1347 (ttp) REVERT: q 338 TRP cc_start: 0.6313 (m100) cc_final: 0.6109 (m100) REVERT: q 404 GLU cc_start: 0.4565 (mp0) cc_final: 0.4321 (pm20) REVERT: q 597 LEU cc_start: -0.1471 (OUTLIER) cc_final: -0.1762 (tp) REVERT: q 644 MET cc_start: 0.1127 (mtm) cc_final: -0.0432 (ttm) REVERT: q 744 MET cc_start: 0.5371 (ppp) cc_final: 0.4617 (pmm) REVERT: q 777 GLU cc_start: 0.8591 (tp30) cc_final: 0.8224 (mm-30) REVERT: q 849 ARG cc_start: 0.7631 (ttt180) cc_final: 0.7323 (ttm170) REVERT: q 911 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6292 (mm-30) REVERT: r 318 ASP cc_start: 0.0968 (m-30) cc_final: 0.0594 (t70) REVERT: r 329 MET cc_start: -0.3514 (tmm) cc_final: -0.3731 (ttp) REVERT: r 401 SER cc_start: 0.9009 (m) cc_final: 0.8650 (p) REVERT: u 171 ILE cc_start: 0.3918 (tp) cc_final: 0.3203 (pt) REVERT: u 255 GLU cc_start: 0.8296 (pm20) cc_final: 0.8062 (pm20) REVERT: u 262 ARG cc_start: 0.8746 (ptp90) cc_final: 0.8408 (ptt90) REVERT: u 265 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9027 (mm-30) REVERT: u 269 ASN cc_start: 0.9120 (m-40) cc_final: 0.8884 (m-40) REVERT: v 63 MET cc_start: 0.4779 (mmm) cc_final: 0.3459 (mpp) REVERT: v 189 ARG cc_start: 0.7906 (tpm170) cc_final: 0.7548 (tpp80) REVERT: v 199 HIS cc_start: 0.4842 (OUTLIER) cc_final: 0.4499 (t-90) REVERT: v 252 PHE cc_start: 0.8850 (m-80) cc_final: 0.8429 (m-80) REVERT: x 233 LYS cc_start: 0.8152 (pttt) cc_final: 0.7784 (pttm) REVERT: x 240 GLU cc_start: 0.6992 (mm-30) cc_final: 0.5923 (mt-10) REVERT: x 246 ASN cc_start: 0.7274 (p0) cc_final: 0.6792 (t0) REVERT: x 279 TRP cc_start: 0.7795 (m100) cc_final: 0.7295 (m100) REVERT: x 303 GLN cc_start: 0.9019 (mp-120) cc_final: 0.8736 (mp10) REVERT: x 319 ASP cc_start: 0.7700 (m-30) cc_final: 0.7254 (m-30) REVERT: x 328 TRP cc_start: 0.6631 (m-10) cc_final: 0.6159 (m-90) REVERT: x 348 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7891 (tt0) REVERT: x 352 ASP cc_start: 0.8297 (m-30) cc_final: 0.7865 (m-30) REVERT: j 541 LYS cc_start: 0.0878 (tmtt) cc_final: 0.0219 (mmmt) REVERT: j 652 MET cc_start: -0.2035 (mpp) cc_final: -0.2596 (ppp) REVERT: k 1 MET cc_start: -0.2697 (OUTLIER) cc_final: -0.2941 (mmt) REVERT: k 21 ARG cc_start: 0.3720 (mtt180) cc_final: 0.3270 (ptt180) REVERT: k 70 ARG cc_start: 0.0506 (ptp-170) cc_final: -0.1091 (tpt170) REVERT: k 86 GLN cc_start: 0.6741 (mt0) cc_final: 0.6311 (pp30) REVERT: k 162 ASN cc_start: 0.3587 (m-40) cc_final: 0.3315 (p0) outliers start: 285 outliers final: 255 residues processed: 1804 average time/residue: 0.7677 time to fit residues: 2375.3483 Evaluate side-chains 1891 residues out of total 8470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1623 time to evaluate : 6.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 300 HIS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 885 ASP Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1335 PHE Chi-restraints excluded: chain A residue 1353 LYS Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain A residue 1408 THR Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1448 ILE Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 696 GLU Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1004 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1032 SER Chi-restraints excluded: chain B residue 1041 GLU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1180 PHE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain K residue 32 ILE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 292 VAL Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 414 VAL Chi-restraints excluded: chain W residue 488 ASN Chi-restraints excluded: chain W residue 512 HIS Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain W residue 598 LEU Chi-restraints excluded: chain W residue 609 VAL Chi-restraints excluded: chain W residue 613 ILE Chi-restraints excluded: chain W residue 618 ASP Chi-restraints excluded: chain W residue 629 LEU Chi-restraints excluded: chain W residue 662 ASP Chi-restraints excluded: chain W residue 675 THR Chi-restraints excluded: chain W residue 755 THR Chi-restraints excluded: chain m residue 294 LEU Chi-restraints excluded: chain m residue 363 PHE Chi-restraints excluded: chain m residue 465 ASP Chi-restraints excluded: chain m residue 542 MET Chi-restraints excluded: chain m residue 553 HIS Chi-restraints excluded: chain m residue 575 ASP Chi-restraints excluded: chain m residue 768 LEU Chi-restraints excluded: chain m residue 774 ASN Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 804 ASP Chi-restraints excluded: chain m residue 835 LEU Chi-restraints excluded: chain m residue 880 THR Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 962 ASN Chi-restraints excluded: chain m residue 1067 ASP Chi-restraints excluded: chain m residue 1085 PHE Chi-restraints excluded: chain m residue 1122 SER Chi-restraints excluded: chain n residue 152 LEU Chi-restraints excluded: chain n residue 185 ILE Chi-restraints excluded: chain n residue 197 ILE Chi-restraints excluded: chain n residue 205 ASP Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 259 VAL Chi-restraints excluded: chain q residue 88 LEU Chi-restraints excluded: chain q residue 118 SER Chi-restraints excluded: chain q residue 350 VAL Chi-restraints excluded: chain q residue 368 LEU Chi-restraints excluded: chain q residue 597 LEU Chi-restraints excluded: chain q residue 631 LEU Chi-restraints excluded: chain q residue 647 THR Chi-restraints excluded: chain q residue 716 LEU Chi-restraints excluded: chain q residue 732 SER Chi-restraints excluded: chain q residue 757 TYR Chi-restraints excluded: chain q residue 767 ASP Chi-restraints excluded: chain q residue 817 GLU Chi-restraints excluded: chain q residue 878 LYS Chi-restraints excluded: chain r residue 221 ASP Chi-restraints excluded: chain r residue 296 HIS Chi-restraints excluded: chain r residue 315 ASP Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 387 LEU Chi-restraints excluded: chain u residue 90 LEU Chi-restraints excluded: chain u residue 107 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 220 LYS Chi-restraints excluded: chain u residue 222 VAL Chi-restraints excluded: chain u residue 229 THR Chi-restraints excluded: chain u residue 232 GLN Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain v residue 136 ASP Chi-restraints excluded: chain v residue 199 HIS Chi-restraints excluded: chain v residue 248 LEU Chi-restraints excluded: chain v residue 257 ILE Chi-restraints excluded: chain v residue 316 ASP Chi-restraints excluded: chain v residue 377 SER Chi-restraints excluded: chain x residue 153 ASN Chi-restraints excluded: chain x residue 163 ASP Chi-restraints excluded: chain x residue 218 SER Chi-restraints excluded: chain x residue 247 LEU Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 296 ASN Chi-restraints excluded: chain x residue 316 TYR Chi-restraints excluded: chain x residue 317 LYS Chi-restraints excluded: chain x residue 345 GLN Chi-restraints excluded: chain x residue 357 THR Chi-restraints excluded: chain j residue 556 ILE Chi-restraints excluded: chain j residue 713 SER Chi-restraints excluded: chain j residue 720 PHE Chi-restraints excluded: chain j residue 747 PHE Chi-restraints excluded: chain j residue 755 VAL Chi-restraints excluded: chain j residue 874 PHE Chi-restraints excluded: chain j residue 893 MET Chi-restraints excluded: chain j residue 913 VAL Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 53 SER Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 77 LEU Chi-restraints excluded: chain k residue 107 LEU Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 172 VAL Chi-restraints excluded: chain k residue 399 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 961 random chunks: chunk 605 optimal weight: 1.9990 chunk 812 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 702 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 763 optimal weight: 20.0000 chunk 319 optimal weight: 0.7980 chunk 784 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 359 ASN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS E 178 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 970 HIS ** n 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 294 HIS ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 859 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.225386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147386 restraints weight = 183719.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142498 restraints weight = 109161.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144041 restraints weight = 74034.770| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 83688 Z= 0.199 Angle : 0.623 18.595 114048 Z= 0.321 Chirality : 0.042 0.353 12699 Planarity : 0.004 0.120 13884 Dihedral : 15.707 128.480 13291 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 2.75 % Allowed : 20.98 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.09), residues: 9398 helix: 1.70 (0.08), residues: 4175 sheet: 0.03 (0.14), residues: 1352 loop : -0.21 (0.10), residues: 3871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP x 292 HIS 0.017 0.001 HIS d 106 PHE 0.035 0.001 PHE m 593 TYR 0.043 0.001 TYR m 313 ARG 0.017 0.000 ARG W 510 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32900.90 seconds wall clock time: 571 minutes 57.70 seconds (34317.70 seconds total)