Starting phenix.real_space_refine on Sat Mar 23 05:24:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wau_37405/03_2024/8wau_37405_trim_updated.pdb" } resolution = 2.78 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= 0.004 sd= 0.125 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: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22150 2.51 5 N 6272 2.21 5 O 6951 1.98 5 H 23 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35721 Number of models: 1 Model: "" Number of chains: 25 Chain: "N" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 87 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'CSX:plan-1': 1, 'HYP:plan-1': 1, 'ILX:plan-1': 1, 'TRX:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain breaks: 1 Chain: "X" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 878 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1112 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 241 Unusual residues: {'ATP': 1} Classifications: {'RNA': 10, 'undetermined': 1} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9, None: 1} Not linked: pdbres="ATP Z 1 " pdbres=" U Z 2 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "o" Number of atoms: 11510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1452, 11510 Classifications: {'peptide': 1452} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1381} Chain breaks: 1 Chain: "p" Number of atoms: 9149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9149 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 53, 'TRANS': 1092} Chain breaks: 1 Chain: "q" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "r" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "u" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "v" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "w" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "x" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "y" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "z" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'W0F': 1} Classifications: {'undetermined': 1} Chain: "o" 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: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "w" 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: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" 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 4709 SG CYS o 71 114.084 112.528 115.101 1.00141.57 S ATOM 4731 SG CYS o 74 111.807 115.440 115.215 1.00137.29 S ATOM 4778 SG CYS o 81 110.391 111.841 114.997 1.00138.71 S ATOM 5013 SG CYS o 111 101.691 111.241 68.337 1.00164.45 S ATOM 5041 SG CYS o 114 103.771 114.633 68.034 1.00163.67 S ATOM 5387 SG CYS o 184 103.785 111.997 65.243 1.00171.81 S ATOM 24474 SG CYS p1119 105.507 124.979 104.004 1.00141.59 S ATOM 24496 SG CYS p1122 105.458 121.777 101.851 1.00142.57 S ATOM 24611 SG CYS p1137 108.325 122.461 103.994 1.00148.67 S ATOM 24632 SG CYS p1140 107.812 124.321 100.753 1.00152.98 S ATOM 25598 SG CYS q 88 85.446 90.728 173.510 1.00138.12 S ATOM 25611 SG CYS q 90 88.897 89.862 172.320 1.00147.15 S ATOM 25646 SG CYS q 94 87.125 87.472 174.632 1.00132.97 S ATOM 25668 SG CYS q 97 85.727 87.800 171.203 1.00132.45 S ATOM 32974 SG CYS w 17 75.543 52.500 55.844 1.00161.53 S ATOM 32998 SG CYS w 20 78.933 53.577 57.374 1.00163.91 S ATOM 33159 SG CYS w 39 76.809 56.290 56.410 1.00169.29 S ATOM 33184 SG CYS w 42 78.072 53.991 53.684 1.00167.79 S ATOM 33536 SG CYS w 86 44.325 43.182 86.150 1.00150.39 S ATOM 33560 SG CYS w 89 44.911 39.705 87.842 1.00155.57 S ATOM 33764 SG CYS w 114 46.645 42.843 89.119 1.00146.35 S ATOM 33799 SG CYS w 119 47.447 41.341 85.663 1.00152.45 S ATOM 33909 SG CYS x 7 65.616 72.329 151.601 1.00 98.61 S ATOM 33933 SG CYS x 10 63.948 73.354 154.825 1.00 95.35 S ATOM 34197 SG CYS x 44 61.770 72.499 151.635 1.00107.46 S ATOM 34203 SG CYS x 45 63.275 70.130 154.051 1.00108.23 S ATOM 35349 SG CYS z 19 107.203 61.353 142.299 1.00146.64 S ATOM 35368 SG CYS z 22 107.999 58.787 144.862 1.00145.85 S ATOM 35485 SG CYS z 36 110.768 61.258 143.920 1.00153.01 S ATOM 35511 SG CYS z 39 109.449 58.883 141.257 1.00150.68 S Time building chain proxies: 18.57, per 1000 atoms: 0.52 Number of scatterers: 35721 At special positions: 0 Unit cell: (165.416, 185.426, 192.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 203 16.00 P 113 15.00 Mg 1 11.99 O 6951 8.00 N 6272 7.00 C 22150 6.00 H 23 1.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.99 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 74 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 184 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb=" ZN p1201 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1140 " pdb="ZN ZN p1201 " - pdb=" SG CYS p1119 " pdb=" ZN q 301 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 94 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 88 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 39 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " Number of angles added : 39 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 44 sheets defined 32.3% alpha, 15.0% beta 43 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 15.19 Creating SS restraints... Processing helix chain 'S' and resid 6 through 8 No H-bonds generated for 'chain 'S' and resid 6 through 8' Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 157 through 165 Processing helix chain 'S' and resid 173 through 179 Processing helix chain 'T' and resid 10 through 14 Processing helix chain 'T' and resid 25 through 34 removed outlier: 4.170A pdb=" N ALA T 34 " --> pdb=" O GLN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 63 No H-bonds generated for 'chain 'T' and resid 60 through 63' Processing helix chain 'o' and resid 28 through 34 Processing helix chain 'o' and resid 99 through 109 Processing helix chain 'o' and resid 124 through 132 Processing helix chain 'o' and resid 137 through 150 removed outlier: 4.270A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.879A pdb=" N ARG o 227 " --> pdb=" O GLU o 223 " (cutoff:3.500A) Processing helix chain 'o' and resid 230 through 236 Processing helix chain 'o' and resid 245 through 248 No H-bonds generated for 'chain 'o' and resid 245 through 248' Processing helix chain 'o' and resid 275 through 296 Processing helix chain 'o' and resid 302 through 318 Processing helix chain 'o' and resid 339 through 343 Processing helix chain 'o' and resid 349 through 352 No H-bonds generated for 'chain 'o' and resid 349 through 352' Processing helix chain 'o' and resid 382 through 387 Processing helix chain 'o' and resid 399 through 408 Processing helix chain 'o' and resid 435 through 438 removed outlier: 3.610A pdb=" N LEU o 438 " --> pdb=" O PRO o 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 435 through 438' Processing helix chain 'o' and resid 466 through 468 No H-bonds generated for 'chain 'o' and resid 466 through 468' Processing helix chain 'o' and resid 486 through 492 removed outlier: 4.095A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 539 through 548 removed outlier: 3.561A pdb=" N LYS o 547 " --> pdb=" O ALA o 544 " (cutoff:3.500A) Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.806A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.865A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.205A pdb=" N SER o 615 " --> pdb=" O ASP o 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 611 through 615' Processing helix chain 'o' and resid 642 through 645 No H-bonds generated for 'chain 'o' and resid 642 through 645' Processing helix chain 'o' and resid 652 through 660 Processing helix chain 'o' and resid 662 through 683 Processing helix chain 'o' and resid 689 through 692 No H-bonds generated for 'chain 'o' and resid 689 through 692' Processing helix chain 'o' and resid 696 through 721 Processing helix chain 'o' and resid 733 through 759 Processing helix chain 'o' and resid 765 through 772 Processing helix chain 'o' and resid 778 through 785 Processing helix chain 'o' and resid 817 through 820 No H-bonds generated for 'chain 'o' and resid 817 through 820' Processing helix chain 'o' and resid 833 through 867 removed outlier: 4.420A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU o 856 " --> pdb=" O VAL o 852 " (cutoff:3.500A) Processing helix chain 'o' and resid 891 through 893 No H-bonds generated for 'chain 'o' and resid 891 through 893' Processing helix chain 'o' and resid 913 through 920 Processing helix chain 'o' and resid 927 through 933 Processing helix chain 'o' and resid 936 through 944 Processing helix chain 'o' and resid 946 through 969 Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1018 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.122A pdb=" N GLN o1101 " --> pdb=" O GLU o1097 " (cutoff:3.500A) Processing helix chain 'o' and resid 1121 through 1129 Processing helix chain 'o' and resid 1151 through 1161 Processing helix chain 'o' and resid 1166 through 1169 No H-bonds generated for 'chain 'o' and resid 1166 through 1169' Processing helix chain 'o' and resid 1188 through 1198 removed outlier: 3.746A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL o1193 " --> pdb=" O GLN o1190 " (cutoff:3.500A) Processing helix chain 'o' and resid 1218 through 1223 Processing helix chain 'o' and resid 1228 through 1239 Processing helix chain 'o' and resid 1263 through 1267 Processing helix chain 'o' and resid 1282 through 1295 Processing helix chain 'o' and resid 1343 through 1348 Processing helix chain 'o' and resid 1362 through 1369 Processing helix chain 'o' and resid 1371 through 1387 Processing helix chain 'o' and resid 1395 through 1406 Processing helix chain 'o' and resid 1416 through 1419 No H-bonds generated for 'chain 'o' and resid 1416 through 1419' Processing helix chain 'o' and resid 1426 through 1431 Processing helix chain 'o' and resid 1435 through 1445 removed outlier: 3.840A pdb=" N MET o1440 " --> pdb=" O ASP o1437 " (cutoff:3.500A) Processing helix chain 'o' and resid 1454 through 1459 Processing helix chain 'o' and resid 1477 through 1481 Processing helix chain 'p' and resid 22 through 36 removed outlier: 3.816A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 61 Processing helix chain 'p' and resid 110 through 115 Processing helix chain 'p' and resid 168 through 173 Processing helix chain 'p' and resid 247 through 252 Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 281 through 288 Processing helix chain 'p' and resid 295 through 307 Proline residue: p 303 - end of helix Processing helix chain 'p' and resid 314 through 323 Processing helix chain 'p' and resid 332 through 345 Processing helix chain 'p' and resid 358 through 377 Processing helix chain 'p' and resid 388 through 390 No H-bonds generated for 'chain 'p' and resid 388 through 390' Processing helix chain 'p' and resid 396 through 425 Processing helix chain 'p' and resid 431 through 434 No H-bonds generated for 'chain 'p' and resid 431 through 434' Processing helix chain 'p' and resid 437 through 450 Processing helix chain 'p' and resid 475 through 482 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 539 through 548 Processing helix chain 'p' and resid 580 through 593 Processing helix chain 'p' and resid 637 through 644 Processing helix chain 'p' and resid 653 through 658 Processing helix chain 'p' and resid 667 through 672 removed outlier: 3.782A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) Processing helix chain 'p' and resid 679 through 682 No H-bonds generated for 'chain 'p' and resid 679 through 682' Processing helix chain 'p' and resid 700 through 703 Processing helix chain 'p' and resid 714 through 716 No H-bonds generated for 'chain 'p' and resid 714 through 716' Processing helix chain 'p' and resid 719 through 731 removed outlier: 3.760A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 762 through 767 Processing helix chain 'p' and resid 798 through 803 Processing helix chain 'p' and resid 969 through 975 Proline residue: p 973 - end of helix Processing helix chain 'p' and resid 978 through 993 Processing helix chain 'p' and resid 1008 through 1018 removed outlier: 3.555A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR p1018 " --> pdb=" O LEU p1014 " (cutoff:3.500A) Processing helix chain 'p' and resid 1055 through 1058 No H-bonds generated for 'chain 'p' and resid 1055 through 1058' Processing helix chain 'p' and resid 1088 through 1097 Processing helix chain 'p' and resid 1100 through 1111 removed outlier: 4.117A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER p1111 " --> pdb=" O LEU p1107 " (cutoff:3.500A) Processing helix chain 'p' and resid 1153 through 1164 Processing helix chain 'q' and resid 28 through 40 Processing helix chain 'q' and resid 61 through 70 Processing helix chain 'q' and resid 78 through 81 No H-bonds generated for 'chain 'q' and resid 78 through 81' Processing helix chain 'q' and resid 117 through 119 No H-bonds generated for 'chain 'q' and resid 117 through 119' Processing helix chain 'q' and resid 174 through 176 No H-bonds generated for 'chain 'q' and resid 174 through 176' Processing helix chain 'q' and resid 200 through 202 No H-bonds generated for 'chain 'q' and resid 200 through 202' Processing helix chain 'q' and resid 241 through 270 removed outlier: 3.562A pdb=" N VAL q 245 " --> pdb=" O PRO q 241 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 27 No H-bonds generated for 'chain 'r' and resid 24 through 27' Processing helix chain 'r' and resid 34 through 50 Processing helix chain 'r' and resid 59 through 70 Processing helix chain 'r' and resid 77 through 89 Processing helix chain 'r' and resid 94 through 103 Processing helix chain 'r' and resid 108 through 114 Processing helix chain 'r' and resid 116 through 118 No H-bonds generated for 'chain 'r' and resid 116 through 118' Processing helix chain 'r' and resid 124 through 137 Processing helix chain 's' and resid 3 through 23 Processing helix chain 's' and resid 30 through 33 No H-bonds generated for 'chain 's' and resid 30 through 33' Processing helix chain 's' and resid 37 through 44 Processing helix chain 's' and resid 84 through 97 Processing helix chain 's' and resid 112 through 120 Processing helix chain 's' and resid 132 through 136 Processing helix chain 's' and resid 139 through 141 No H-bonds generated for 'chain 's' and resid 139 through 141' Processing helix chain 's' and resid 153 through 162 Processing helix chain 's' and resid 178 through 183 Processing helix chain 't' and resid 59 through 75 Processing helix chain 't' and resid 89 through 99 Processing helix chain 'u' and resid 15 through 17 No H-bonds generated for 'chain 'u' and resid 15 through 17' Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'w' and resid 70 through 74 Processing helix chain 'x' and resid 18 through 27 Processing helix chain 'x' and resid 31 through 38 Processing helix chain 'x' and resid 43 through 50 removed outlier: 3.606A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.688A pdb=" N ASN x 61 " --> pdb=" O GLU x 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 9 Processing helix chain 'y' and resid 40 through 52 removed outlier: 3.828A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 112 Processing sheet with id= A, first strand: chain 'S' and resid 27 through 31 removed outlier: 6.827A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 125 through 128 removed outlier: 3.581A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.281A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU T 115 " --> pdb=" O LYS T 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'T' and resid 94 through 98 removed outlier: 3.602A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU T 106 " --> pdb=" O THR T 97 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'o' and resid 86 through 89 Processing sheet with id= F, first strand: chain 'o' and resid 190 through 194 removed outlier: 4.618A pdb=" N LEU o 198 " --> pdb=" O LEU o 216 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'o' and resid 264 through 266 Processing sheet with id= H, first strand: chain 'o' and resid 362 through 366 removed outlier: 3.549A pdb=" N THR o 365 " --> pdb=" O MET o 501 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'o' and resid 367 through 369 removed outlier: 6.103A pdb=" N PHE o 482 " --> pdb=" O THR o 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'o' and resid 389 through 393 removed outlier: 3.896A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA o 416 " --> pdb=" O HIS o 449 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'o' and resid 602 through 604 removed outlier: 3.576A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU o 635 " --> pdb=" O GLU o 631 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'o' and resid 902 through 905 Processing sheet with id= M, first strand: chain 'o' and resid 1138 through 1142 removed outlier: 3.659A pdb=" N LYS o1306 " --> pdb=" O ASP o1339 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'o' and resid 1244 through 1247 removed outlier: 4.353A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA o1174 " --> pdb=" O ARG o1213 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'o' and resid 1319 through 1322 Processing sheet with id= P, first strand: chain 'p' and resid 65 through 67 Processing sheet with id= Q, first strand: chain 'p' and resid 91 through 93 removed outlier: 3.744A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE p 148 " --> pdb=" O VAL p 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'p' and resid 97 through 99 Processing sheet with id= S, first strand: chain 'p' and resid 185 through 187 Processing sheet with id= T, first strand: chain 'p' and resid 197 through 200 Processing sheet with id= U, first strand: chain 'p' and resid 205 through 208 removed outlier: 6.873A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'p' and resid 484 through 486 Processing sheet with id= W, first strand: chain 'p' and resid 530 through 532 Processing sheet with id= X, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.535A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL p 904 " --> pdb=" O ARG p 924 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'p' and resid 945 through 949 removed outlier: 6.907A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'p' and resid 827 through 829 Processing sheet with id= AA, first strand: chain 'p' and resid 1113 through 1119 Processing sheet with id= AB, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id= AC, first strand: chain 'q' and resid 182 through 185 removed outlier: 6.809A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL q 9 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 98 through 106 removed outlier: 6.081A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE q 45 " --> pdb=" O GLY q 168 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 113 through 116 Processing sheet with id= AF, first strand: chain 's' and resid 60 through 62 removed outlier: 6.265A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 's' and resid 147 through 150 removed outlier: 3.648A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 't' and resid 105 through 109 Processing sheet with id= AI, first strand: chain 'u' and resid 2 through 13 Processing sheet with id= AJ, first strand: chain 'u' and resid 142 through 146 removed outlier: 7.009A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER u 105 " --> pdb=" O ILE u 157 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE u 147 " --> pdb=" O SER u 162 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'u' and resid 127 through 129 Processing sheet with id= AL, first strand: chain 'u' and resid 44 through 48 removed outlier: 6.852A pdb=" N ILE u 75 " --> pdb=" O ILE u 46 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'u' and resid 50 through 54 removed outlier: 6.844A pdb=" N LYS u 71 " --> pdb=" O ASP u 52 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'v' and resid 25 through 31 removed outlier: 5.247A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'w' and resid 24 through 28 Processing sheet with id= AP, first strand: chain 'w' and resid 79 through 81 Processing sheet with id= AQ, first strand: chain 'y' and resid 19 through 23 Processing sheet with id= AR, first strand: chain 'z' and resid 16 through 18 1151 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 17.00 Time building geometry restraints manager: 16.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 23 1.17 - 1.33: 9014 1.33 - 1.49: 12403 1.49 - 1.65: 14855 1.65 - 1.81: 325 Bond restraints: 36620 Sorted by residual: bond pdb=" C4' G2L Z 11 " pdb=" C3' G2L Z 11 " ideal model delta sigma weight residual 1.270 1.524 -0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C2' G2L Z 11 " pdb=" C1' G2L Z 11 " ideal model delta sigma weight residual 1.271 1.480 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" P G2L Z 11 " pdb=" O5' G2L Z 11 " ideal model delta sigma weight residual 1.685 1.496 0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C4' G2L Z 11 " pdb=" O4' G2L Z 11 " ideal model delta sigma weight residual 1.560 1.394 0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" N GLY N 3 " pdb=" H GLY N 3 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 36615 not shown) Histogram of bond angle deviations from ideal: 75.41 - 88.77: 3 88.77 - 102.13: 285 102.13 - 115.49: 24080 115.49 - 128.85: 25286 128.85 - 142.21: 309 Bond angle restraints: 49963 Sorted by residual: angle pdb=" O3' A Z 10 " pdb=" P G2L Z 11 " pdb=" O5' G2L Z 11 " ideal model delta sigma weight residual 104.00 76.36 27.64 1.50e+00 4.44e-01 3.40e+02 angle pdb=" N09 W0F Z2500 " pdb=" C06 W0F Z2500 " pdb=" O05 W0F Z2500 " ideal model delta sigma weight residual 110.18 75.41 34.77 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C07 W0F Z2500 " pdb=" C06 W0F Z2500 " pdb=" N09 W0F Z2500 " ideal model delta sigma weight residual 110.46 136.30 -25.84 3.00e+00 1.11e-01 7.42e+01 angle pdb=" C5' G2L Z 11 " pdb=" C4' G2L Z 11 " pdb=" O4' G2L Z 11 " ideal model delta sigma weight residual 110.08 87.22 22.86 3.00e+00 1.11e-01 5.81e+01 angle pdb=" P26 W0F Z2500 " pdb=" O29 W0F Z2500 " pdb=" P30 W0F Z2500 " ideal model delta sigma weight residual 123.60 142.21 -18.61 3.00e+00 1.11e-01 3.85e+01 ... (remaining 49958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 21375 35.97 - 71.93: 727 71.93 - 107.90: 31 107.90 - 143.86: 0 143.86 - 179.83: 1 Dihedral angle restraints: 22134 sinusoidal: 9974 harmonic: 12160 Sorted by residual: dihedral pdb=" CA TRP o 479 " pdb=" C TRP o 479 " pdb=" N SER o 480 " pdb=" CA SER o 480 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA LEU o 343 " pdb=" C LEU o 343 " pdb=" N LYS o 344 " pdb=" CA LYS o 344 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA VAL o1341 " pdb=" C VAL o1341 " pdb=" N SER o1342 " pdb=" CA SER o1342 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 22131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4868 0.074 - 0.148: 667 0.148 - 0.223: 15 0.223 - 0.297: 4 0.297 - 0.371: 3 Chirality restraints: 5557 Sorted by residual: chirality pdb=" C06 W0F Z2500 " pdb=" C07 W0F Z2500 " pdb=" N09 W0F Z2500 " pdb=" O05 W0F Z2500 " both_signs ideal model delta sigma weight residual False 2.41 2.04 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA HYP N 8 " pdb=" N HYP N 8 " pdb=" C HYP N 8 " pdb=" CB HYP N 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C03 W0F Z2500 " pdb=" C04 W0F Z2500 " pdb=" C07 W0F Z2500 " pdb=" O02 W0F Z2500 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 5554 not shown) Planarity restraints: 6101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F Z2500 " -0.108 2.00e-02 2.50e+03 4.13e-02 5.12e+01 pdb=" C10 W0F Z2500 " 0.040 2.00e-02 2.50e+03 pdb=" C12 W0F Z2500 " 0.007 2.00e-02 2.50e+03 pdb=" C13 W0F Z2500 " 0.031 2.00e-02 2.50e+03 pdb=" C15 W0F Z2500 " 0.008 2.00e-02 2.50e+03 pdb=" C17 W0F Z2500 " -0.020 2.00e-02 2.50e+03 pdb=" N09 W0F Z2500 " 0.052 2.00e-02 2.50e+03 pdb=" N11 W0F Z2500 " 0.013 2.00e-02 2.50e+03 pdb=" N14 W0F Z2500 " 0.031 2.00e-02 2.50e+03 pdb=" N16 W0F Z2500 " -0.017 2.00e-02 2.50e+03 pdb=" N19 W0F Z2500 " 0.006 2.00e-02 2.50e+03 pdb=" O18 W0F Z2500 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ILE p 51 " 0.078 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE p 50 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C PHE p 50 " 0.070 2.00e-02 2.50e+03 pdb=" O PHE p 50 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE p 51 " -0.024 2.00e-02 2.50e+03 ... (remaining 6098 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.40: 46 2.40 - 2.95: 16263 2.95 - 3.50: 41251 3.50 - 4.05: 70531 4.05 - 4.60: 102001 Nonbonded interactions: 230092 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.850 2.050 nonbonded pdb=" C10 W0F Z2500 " pdb=" O05 W0F Z2500 " model vdw 1.871 2.520 nonbonded pdb=" OD1 ASP o 497 " pdb="MG MG o2003 " model vdw 1.922 2.050 nonbonded pdb="HG22 ILE N 4 " pdb="HD13 ILE N 4 " model vdw 2.018 2.440 nonbonded pdb=" OD2 ASP o 497 " pdb=" O33 W0F Z2500 " model vdw 2.035 2.800 ... (remaining 230087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.950 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: 0.730 Extract box with map and model: 8.680 Check model and map are aligned: 0.460 Set scattering table: 0.330 Process input model: 110.420 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5224 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 : 0.008 0.254 36597 Z= 0.503 Angle : 0.807 34.769 49911 Z= 0.411 Chirality : 0.048 0.371 5557 Planarity : 0.005 0.058 6097 Dihedral : 15.383 179.829 14261 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 1.38 % Allowed : 5.99 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.44 (0.13), residues: 4137 helix: 1.22 (0.14), residues: 1416 sheet: 0.21 (0.20), residues: 685 loop : -0.27 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP o1192 HIS 0.008 0.001 HIS o 809 PHE 0.020 0.002 PHE q 93 TYR 0.031 0.002 TYR o 669 ARG 0.008 0.001 ARG p 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 956 time to evaluate : 4.081 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: o 18 ILE cc_start: 0.7787 (mt) cc_final: 0.7328 (mm) REVERT: o 38 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6818 (mm-30) REVERT: o 48 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: o 54 LEU cc_start: 0.6904 (mt) cc_final: 0.6699 (mt) REVERT: o 58 MET cc_start: 0.7731 (ttp) cc_final: 0.7511 (ttm) REVERT: o 67 ARG cc_start: 0.8377 (ttp80) cc_final: 0.7189 (tpp-160) REVERT: o 92 LYS cc_start: 0.8086 (mtpp) cc_final: 0.7737 (mttm) REVERT: o 103 THR cc_start: 0.7438 (m) cc_final: 0.7155 (m) REVERT: o 193 ARG cc_start: 0.7248 (ttp80) cc_final: 0.6972 (ttt90) REVERT: o 194 SER cc_start: 0.7356 (t) cc_final: 0.6606 (p) REVERT: o 196 LEU cc_start: 0.8608 (mt) cc_final: 0.8369 (mm) REVERT: o 197 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6833 (pt0) REVERT: o 226 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7442 (ttpt) REVERT: o 266 MET cc_start: 0.3400 (mtm) cc_final: 0.2350 (tmm) REVERT: o 274 ASP cc_start: 0.6134 (t0) cc_final: 0.5908 (t70) REVERT: o 347 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7406 (mp0) REVERT: o 403 GLN cc_start: 0.5707 (tt0) cc_final: 0.5490 (tp40) REVERT: o 426 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6515 (mtm-85) REVERT: o 451 CYS cc_start: 0.6959 (m) cc_final: 0.6566 (p) REVERT: o 467 MET cc_start: 0.7191 (mmt) cc_final: 0.6717 (mmt) REVERT: o 473 ARG cc_start: 0.6647 (ttp-170) cc_final: 0.6149 (ttm-80) REVERT: o 495 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6459 (p0) REVERT: o 508 SER cc_start: 0.6254 (t) cc_final: 0.6042 (m) REVERT: o 524 MET cc_start: 0.8052 (mmp) cc_final: 0.7638 (mmp) REVERT: o 556 GLU cc_start: 0.6620 (pt0) cc_final: 0.6029 (tp30) REVERT: o 612 ASP cc_start: 0.7338 (m-30) cc_final: 0.6987 (p0) REVERT: o 691 ASP cc_start: 0.7607 (m-30) cc_final: 0.7282 (m-30) REVERT: o 728 THR cc_start: 0.7387 (m) cc_final: 0.6897 (t) REVERT: o 796 LYS cc_start: 0.7157 (mttt) cc_final: 0.6696 (mttm) REVERT: o 803 LYS cc_start: 0.7398 (tttp) cc_final: 0.7006 (tptp) REVERT: o 818 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7434 (mp0) REVERT: o 841 MET cc_start: 0.7040 (mtp) cc_final: 0.6773 (mtm) REVERT: o 868 MET cc_start: 0.7383 (ptt) cc_final: 0.6908 (ptm) REVERT: o 902 GLU cc_start: 0.6199 (tt0) cc_final: 0.5755 (mt-10) REVERT: o 913 ASN cc_start: 0.6239 (m-40) cc_final: 0.5908 (m-40) REVERT: o 919 LYS cc_start: 0.6166 (mttt) cc_final: 0.5911 (mmtt) REVERT: o 924 TYR cc_start: 0.6880 (p90) cc_final: 0.6653 (p90) REVERT: o 926 ASN cc_start: 0.6522 (m-40) cc_final: 0.6286 (t0) REVERT: o 953 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6209 (mm-30) REVERT: o 958 ARG cc_start: 0.5738 (mtt180) cc_final: 0.5532 (mtm110) REVERT: o 962 ASP cc_start: 0.7006 (m-30) cc_final: 0.6643 (m-30) REVERT: o 976 LYS cc_start: 0.7168 (ttmt) cc_final: 0.6382 (tptt) REVERT: o 1054 MET cc_start: 0.7497 (mmt) cc_final: 0.7174 (mmp) REVERT: o 1063 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6450 (pt0) REVERT: o 1085 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6478 (mm-30) REVERT: o 1132 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7417 (mmtm) REVERT: o 1133 LYS cc_start: 0.7872 (mttt) cc_final: 0.7537 (mmtm) REVERT: o 1135 LYS cc_start: 0.7703 (mttt) cc_final: 0.7249 (tppt) REVERT: o 1144 LEU cc_start: 0.7712 (tp) cc_final: 0.7376 (tm) REVERT: o 1167 ARG cc_start: 0.6829 (ttp-110) cc_final: 0.6457 (ttm-80) REVERT: o 1168 LYS cc_start: 0.7894 (mttt) cc_final: 0.7673 (mtpp) REVERT: o 1169 VAL cc_start: 0.7127 (m) cc_final: 0.6866 (p) REVERT: o 1173 THR cc_start: 0.7730 (m) cc_final: 0.7279 (t) REVERT: o 1217 ASP cc_start: 0.5893 (t0) cc_final: 0.5350 (t0) REVERT: o 1262 MET cc_start: 0.6762 (ttt) cc_final: 0.6344 (tpp) REVERT: o 1302 GLU cc_start: 0.7295 (pt0) cc_final: 0.6561 (mp0) REVERT: o 1303 GLN cc_start: 0.7886 (mt0) cc_final: 0.7653 (mp10) REVERT: o 1306 LYS cc_start: 0.6109 (mttt) cc_final: 0.5276 (mmtm) REVERT: o 1310 HIS cc_start: 0.6721 (p-80) cc_final: 0.6345 (p-80) REVERT: o 1321 ILE cc_start: 0.7605 (mt) cc_final: 0.7395 (pt) REVERT: o 1325 ASP cc_start: 0.6571 (m-30) cc_final: 0.6312 (m-30) REVERT: o 1334 TRP cc_start: 0.8700 (m100) cc_final: 0.8444 (m100) REVERT: o 1337 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6117 (mt-10) REVERT: o 1339 ASP cc_start: 0.6654 (t0) cc_final: 0.6283 (m-30) REVERT: o 1344 MET cc_start: 0.7146 (tpp) cc_final: 0.6841 (tpt) REVERT: o 1350 LYS cc_start: 0.7214 (tttm) cc_final: 0.6932 (ttmt) REVERT: o 1376 LYS cc_start: 0.6559 (ttmm) cc_final: 0.6083 (tttm) REVERT: o 1422 GLN cc_start: 0.7028 (mt0) cc_final: 0.6254 (mm110) REVERT: o 1452 LYS cc_start: 0.6772 (mttt) cc_final: 0.6483 (mmtt) REVERT: o 1472 ASP cc_start: 0.6540 (t0) cc_final: 0.6129 (m-30) REVERT: p 17 ILE cc_start: 0.8149 (mt) cc_final: 0.7845 (mm) REVERT: p 200 MET cc_start: 0.7892 (ttm) cc_final: 0.7648 (ttm) REVERT: p 215 TYR cc_start: 0.6910 (m-80) cc_final: 0.6236 (m-80) REVERT: p 222 ARG cc_start: 0.6334 (mtp-110) cc_final: 0.5745 (mtp85) REVERT: p 239 MET cc_start: 0.6922 (ttm) cc_final: 0.6548 (ttp) REVERT: p 254 GLN cc_start: 0.5996 (mt0) cc_final: 0.5647 (mp10) REVERT: p 295 PRO cc_start: 0.7831 (Cg_endo) cc_final: 0.7408 (Cg_exo) REVERT: p 307 GLU cc_start: 0.8503 (tp30) cc_final: 0.8276 (tp30) REVERT: p 335 ARG cc_start: 0.7035 (mtm180) cc_final: 0.6441 (mtp180) REVERT: p 358 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6618 (pm20) REVERT: p 382 LEU cc_start: 0.8062 (mt) cc_final: 0.7861 (mm) REVERT: p 546 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6464 (mt-10) REVERT: p 574 VAL cc_start: 0.7908 (t) cc_final: 0.7532 (m) REVERT: p 577 HIS cc_start: 0.7562 (t-170) cc_final: 0.7221 (t70) REVERT: p 606 ASP cc_start: 0.6675 (t0) cc_final: 0.5838 (t0) REVERT: p 609 GLU cc_start: 0.6219 (mp0) cc_final: 0.5960 (mp0) REVERT: p 636 LYS cc_start: 0.5944 (mttt) cc_final: 0.5545 (mmtt) REVERT: p 684 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6210 (pt0) REVERT: p 728 MET cc_start: 0.7106 (mtm) cc_final: 0.6625 (mtp) REVERT: p 733 MET cc_start: 0.8485 (mtt) cc_final: 0.8185 (mtm) REVERT: p 737 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7145 (tp) REVERT: p 761 THR cc_start: 0.7800 (m) cc_final: 0.7558 (m) REVERT: p 796 MET cc_start: 0.8723 (mtm) cc_final: 0.8218 (mtm) REVERT: p 817 GLN cc_start: 0.6211 (tt0) cc_final: 0.5739 (pm20) REVERT: p 850 ASP cc_start: 0.7802 (t0) cc_final: 0.7159 (p0) REVERT: p 859 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7544 (ttm170) REVERT: p 866 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7251 (pt) REVERT: p 897 ARG cc_start: 0.5827 (mmt90) cc_final: 0.5475 (mmm160) REVERT: p 914 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6247 (tm-30) REVERT: p 958 CYS cc_start: 0.7249 (m) cc_final: 0.6941 (p) REVERT: p 959 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7191 (mt-10) REVERT: p 995 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7277 (pp20) REVERT: p 1054 MET cc_start: 0.8187 (mtm) cc_final: 0.7592 (mtm) REVERT: p 1076 GLU cc_start: 0.8053 (tt0) cc_final: 0.7323 (tm-30) REVERT: p 1080 ARG cc_start: 0.7375 (mtt90) cc_final: 0.7062 (mtm180) REVERT: p 1115 GLN cc_start: 0.7968 (mt0) cc_final: 0.7646 (mt0) REVERT: p 1121 LEU cc_start: 0.7784 (mt) cc_final: 0.7543 (mt) REVERT: p 1143 LYS cc_start: 0.6360 (tttp) cc_final: 0.6068 (mmtm) REVERT: p 1147 SER cc_start: 0.8227 (m) cc_final: 0.7857 (p) REVERT: p 1150 ARG cc_start: 0.7295 (mtt180) cc_final: 0.6897 (mmm160) REVERT: p 1151 MET cc_start: 0.7950 (ptm) cc_final: 0.7378 (ptp) REVERT: p 1172 MET cc_start: 0.7083 (mmt) cc_final: 0.6694 (mmt) REVERT: q 17 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6679 (mp0) REVERT: q 81 LYS cc_start: 0.6787 (mtpt) cc_final: 0.6173 (mttt) REVERT: q 83 GLN cc_start: 0.7897 (mt0) cc_final: 0.7611 (mt0) REVERT: q 93 PHE cc_start: 0.6921 (m-80) cc_final: 0.6386 (m-80) REVERT: q 96 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5959 (mp0) REVERT: q 102 THR cc_start: 0.7645 (m) cc_final: 0.7247 (p) REVERT: q 106 ARG cc_start: 0.7480 (ttt180) cc_final: 0.7116 (ttp80) REVERT: q 108 ASN cc_start: 0.7295 (m-40) cc_final: 0.6977 (p0) REVERT: q 109 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6580 (pm20) REVERT: q 121 ILE cc_start: 0.8158 (mt) cc_final: 0.7833 (mm) REVERT: q 126 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6780 (mmm160) REVERT: q 215 GLU cc_start: 0.6326 (mt-10) cc_final: 0.6032 (mt-10) REVERT: q 253 LYS cc_start: 0.6858 (tttt) cc_final: 0.6524 (ttmt) REVERT: q 254 LYS cc_start: 0.6095 (tttt) cc_final: 0.5718 (mptt) REVERT: r 62 MET cc_start: 0.7657 (mmt) cc_final: 0.7260 (mmm) REVERT: s 4 GLU cc_start: 0.7221 (tt0) cc_final: 0.7015 (tp30) REVERT: s 38 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7289 (mm-30) REVERT: s 41 LYS cc_start: 0.5973 (mtmm) cc_final: 0.5629 (mtpp) REVERT: s 47 LYS cc_start: 0.7666 (pttm) cc_final: 0.7166 (pmtt) REVERT: s 48 PRO cc_start: 0.8572 (Cg_endo) cc_final: 0.8340 (Cg_exo) REVERT: s 79 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6705 (mp0) REVERT: s 115 LYS cc_start: 0.5783 (mttt) cc_final: 0.5570 (mttp) REVERT: s 133 GLN cc_start: 0.6943 (mt0) cc_final: 0.6652 (tp-100) REVERT: s 138 ASN cc_start: 0.7421 (t0) cc_final: 0.7066 (t0) REVERT: s 195 ARG cc_start: 0.7517 (ptt-90) cc_final: 0.7249 (ptt90) REVERT: s 197 SER cc_start: 0.8897 (t) cc_final: 0.8641 (t) REVERT: s 210 GLN cc_start: 0.6578 (mt0) cc_final: 0.6081 (tm-30) REVERT: t 57 MET cc_start: 0.6944 (ttp) cc_final: 0.6657 (ttm) REVERT: t 79 VAL cc_start: 0.7175 (t) cc_final: 0.6400 (p) REVERT: t 80 MET cc_start: 0.7490 (mmt) cc_final: 0.5936 (mmt) REVERT: t 86 GLU cc_start: 0.6701 (mm-30) cc_final: 0.6416 (mm-30) REVERT: t 98 LYS cc_start: 0.7761 (mttt) cc_final: 0.7540 (mtmm) REVERT: t 117 ASP cc_start: 0.7578 (m-30) cc_final: 0.7298 (m-30) REVERT: u 76 VAL cc_start: 0.6943 (m) cc_final: 0.6715 (m) REVERT: v 35 PHE cc_start: 0.7583 (m-80) cc_final: 0.7357 (m-10) REVERT: v 36 LYS cc_start: 0.6578 (tptt) cc_final: 0.6279 (mmtt) REVERT: v 51 ASP cc_start: 0.7149 (m-30) cc_final: 0.6224 (p0) REVERT: v 63 THR cc_start: 0.8915 (p) cc_final: 0.8579 (t) REVERT: v 71 ASP cc_start: 0.6417 (m-30) cc_final: 0.5705 (m-30) REVERT: v 79 ASP cc_start: 0.5901 (m-30) cc_final: 0.5466 (t0) REVERT: v 95 LYS cc_start: 0.6551 (tttt) cc_final: 0.6124 (ttmt) REVERT: v 100 GLU cc_start: 0.7083 (tt0) cc_final: 0.6054 (mt-10) REVERT: v 110 THR cc_start: 0.7745 (p) cc_final: 0.7078 (p) REVERT: v 126 GLN cc_start: 0.7132 (tt0) cc_final: 0.6515 (tt0) REVERT: v 136 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7149 (mt-10) REVERT: v 146 LYS cc_start: 0.6490 (tttt) cc_final: 0.6067 (tttm) REVERT: w 23 MET cc_start: 0.7496 (ttm) cc_final: 0.7276 (ttp) REVERT: w 25 TYR cc_start: 0.7754 (m-80) cc_final: 0.7536 (m-80) REVERT: w 34 ILE cc_start: 0.6078 (mt) cc_final: 0.5811 (pt) REVERT: w 56 ASN cc_start: 0.7411 (t0) cc_final: 0.7160 (t0) REVERT: w 71 ASP cc_start: 0.7548 (m-30) cc_final: 0.7163 (m-30) REVERT: w 92 LYS cc_start: 0.7098 (mttt) cc_final: 0.6720 (mmtp) REVERT: w 93 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7015 (mt-10) REVERT: w 115 THR cc_start: 0.7978 (m) cc_final: 0.7572 (p) REVERT: x 26 GLN cc_start: 0.7345 (mm-40) cc_final: 0.7074 (mt0) REVERT: x 62 TYR cc_start: 0.7648 (m-80) cc_final: 0.7147 (m-80) REVERT: y 8 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6749 (mm-30) REVERT: y 23 LYS cc_start: 0.7963 (mttt) cc_final: 0.7241 (mmtt) REVERT: y 32 LEU cc_start: 0.7351 (tp) cc_final: 0.7057 (mt) REVERT: y 38 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7169 (mm-30) REVERT: y 85 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6428 (tt0) REVERT: z 16 ILE cc_start: 0.8302 (mt) cc_final: 0.7795 (mp) REVERT: z 25 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6002 (mp0) REVERT: z 35 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7551 (ttp80) REVERT: z 53 VAL cc_start: 0.8666 (t) cc_final: 0.8426 (p) outliers start: 51 outliers final: 8 residues processed: 987 average time/residue: 1.6941 time to fit residues: 1965.8107 Evaluate side-chains 611 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 599 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain o residue 48 GLU Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 1291 ASN Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 737 ILE Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain y residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 2.9990 chunk 319 optimal weight: 0.0070 chunk 177 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 170 optimal weight: 0.5980 chunk 329 optimal weight: 50.0000 chunk 127 optimal weight: 0.4980 chunk 200 optimal weight: 0.7980 chunk 245 optimal weight: 0.5980 chunk 382 optimal weight: 4.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 178 GLN o 62 GLN o 181 HIS o 301 HIS ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 531 ASN ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 721 HIS o 765 ASN o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 904 GLN o 945 ASN o1044 HIS ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1230 GLN o1410 HIS o1462 GLN p 43 GLN p 56 GLN p 98 HIS p 144 HIS p 145 GLN p 164 ASN p 245 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 525 ASN p 537 GLN p 639 HIS p 650 ASN p 699 HIS p 838 GLN p 941 GLN p 948 GLN p1007 ASN p1021 HIS p1068 GLN p1133 HIS q 18 ASN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN r 66 ASN r 129 GLN s 64 HIS t 46 GLN u 14 HIS u 24 ASN u 28 GLN v 44 ASN w 22 ASN w 45 GLN w 50 ASN w 74 GLN w 98 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5252 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36597 Z= 0.162 Angle : 0.479 9.372 49911 Z= 0.259 Chirality : 0.040 0.162 5557 Planarity : 0.003 0.042 6097 Dihedral : 16.699 177.016 5828 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 3.04 % Allowed : 14.53 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.89 (0.13), residues: 4137 helix: 1.82 (0.14), residues: 1410 sheet: 0.23 (0.19), residues: 695 loop : -0.08 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP o1192 HIS 0.010 0.001 HIS r 43 PHE 0.016 0.001 PHE o 234 TYR 0.021 0.001 TYR p 84 ARG 0.012 0.000 ARG p 975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 635 time to evaluate : 4.057 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: o 16 ARG cc_start: 0.7388 (mmt90) cc_final: 0.6941 (mtt-85) REVERT: o 18 ILE cc_start: 0.7620 (mt) cc_final: 0.7318 (mm) REVERT: o 48 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: o 58 MET cc_start: 0.7785 (ttp) cc_final: 0.7569 (ttm) REVERT: o 67 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7006 (tpp-160) REVERT: o 103 THR cc_start: 0.7571 (m) cc_final: 0.7318 (m) REVERT: o 105 LYS cc_start: 0.4914 (OUTLIER) cc_final: 0.4662 (ttmm) REVERT: o 193 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6969 (ttt180) REVERT: o 194 SER cc_start: 0.7335 (t) cc_final: 0.6654 (p) REVERT: o 197 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6825 (pt0) REVERT: o 199 TYR cc_start: 0.7434 (m-80) cc_final: 0.6917 (m-80) REVERT: o 226 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7400 (ttpt) REVERT: o 266 MET cc_start: 0.2687 (mtm) cc_final: 0.1982 (tmm) REVERT: o 329 MET cc_start: 0.5647 (mpp) cc_final: 0.5341 (mmm) REVERT: o 347 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7384 (mp0) REVERT: o 387 ASN cc_start: 0.7332 (m-40) cc_final: 0.7130 (t160) REVERT: o 411 SER cc_start: 0.7943 (m) cc_final: 0.7693 (p) REVERT: o 423 ASN cc_start: 0.7527 (OUTLIER) cc_final: 0.7010 (p0) REVERT: o 426 ARG cc_start: 0.6961 (mtm180) cc_final: 0.6725 (mtm-85) REVERT: o 451 CYS cc_start: 0.6979 (m) cc_final: 0.6426 (p) REVERT: o 467 MET cc_start: 0.7271 (mmt) cc_final: 0.6754 (mmt) REVERT: o 473 ARG cc_start: 0.6658 (ttp-170) cc_final: 0.6143 (ttm-80) REVERT: o 495 ASP cc_start: 0.6424 (OUTLIER) cc_final: 0.6168 (p0) REVERT: o 508 SER cc_start: 0.6089 (t) cc_final: 0.5879 (m) REVERT: o 524 MET cc_start: 0.8026 (mmp) cc_final: 0.7601 (mmp) REVERT: o 561 MET cc_start: 0.7571 (mtt) cc_final: 0.7226 (mmm) REVERT: o 612 ASP cc_start: 0.7326 (m-30) cc_final: 0.7022 (p0) REVERT: o 691 ASP cc_start: 0.7720 (m-30) cc_final: 0.7476 (m-30) REVERT: o 728 THR cc_start: 0.7541 (m) cc_final: 0.7027 (t) REVERT: o 762 GLU cc_start: 0.8007 (mp0) cc_final: 0.7484 (mm-30) REVERT: o 796 LYS cc_start: 0.7065 (mttt) cc_final: 0.6651 (mttm) REVERT: o 803 LYS cc_start: 0.7402 (tttp) cc_final: 0.7009 (tptp) REVERT: o 818 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7441 (mp0) REVERT: o 868 MET cc_start: 0.7402 (ptt) cc_final: 0.6904 (ptm) REVERT: o 902 GLU cc_start: 0.6281 (tt0) cc_final: 0.5691 (mt-10) REVERT: o 919 LYS cc_start: 0.6052 (mttt) cc_final: 0.5807 (mmtt) REVERT: o 953 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6188 (mm-30) REVERT: o 962 ASP cc_start: 0.7096 (m-30) cc_final: 0.6703 (m-30) REVERT: o 976 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6404 (tptt) REVERT: o 1015 GLU cc_start: 0.5491 (mt-10) cc_final: 0.5287 (mm-30) REVERT: o 1063 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6229 (pt0) REVERT: o 1085 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6403 (mm-30) REVERT: o 1133 LYS cc_start: 0.7849 (mttt) cc_final: 0.7579 (mtmm) REVERT: o 1135 LYS cc_start: 0.7495 (mttt) cc_final: 0.7230 (tppt) REVERT: o 1144 LEU cc_start: 0.7833 (tp) cc_final: 0.7552 (tm) REVERT: o 1167 ARG cc_start: 0.7008 (ttp-110) cc_final: 0.6453 (ttm-80) REVERT: o 1168 LYS cc_start: 0.8013 (mttt) cc_final: 0.7667 (mtpp) REVERT: o 1217 ASP cc_start: 0.5794 (t0) cc_final: 0.5335 (t0) REVERT: o 1262 MET cc_start: 0.6636 (ttt) cc_final: 0.6298 (tpp) REVERT: o 1302 GLU cc_start: 0.7280 (pt0) cc_final: 0.6749 (mp0) REVERT: o 1303 GLN cc_start: 0.7900 (mt0) cc_final: 0.7609 (mp10) REVERT: o 1306 LYS cc_start: 0.6055 (mttt) cc_final: 0.5208 (mmtm) REVERT: o 1310 HIS cc_start: 0.6826 (p-80) cc_final: 0.6581 (p-80) REVERT: o 1334 TRP cc_start: 0.8722 (m100) cc_final: 0.8413 (m100) REVERT: o 1337 GLU cc_start: 0.6269 (mt-10) cc_final: 0.5945 (mm-30) REVERT: o 1344 MET cc_start: 0.6559 (tpp) cc_final: 0.6214 (tpt) REVERT: o 1376 LYS cc_start: 0.6483 (ttmm) cc_final: 0.6219 (tptm) REVERT: o 1422 GLN cc_start: 0.6928 (mt0) cc_final: 0.6212 (mm110) REVERT: o 1452 LYS cc_start: 0.6799 (mttt) cc_final: 0.6443 (mmtt) REVERT: p 36 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: p 200 MET cc_start: 0.7888 (ttm) cc_final: 0.7613 (ttm) REVERT: p 215 TYR cc_start: 0.6858 (m-80) cc_final: 0.6032 (m-80) REVERT: p 239 MET cc_start: 0.6932 (ttm) cc_final: 0.6565 (ttp) REVERT: p 307 GLU cc_start: 0.8375 (tp30) cc_final: 0.7664 (tp30) REVERT: p 312 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6639 (tm-30) REVERT: p 335 ARG cc_start: 0.7059 (mtm180) cc_final: 0.6389 (mtp180) REVERT: p 358 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6670 (pm20) REVERT: p 546 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6434 (mt-10) REVERT: p 563 ASP cc_start: 0.3842 (m-30) cc_final: 0.2882 (m-30) REVERT: p 578 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7343 (mmtt) REVERT: p 606 ASP cc_start: 0.6659 (t0) cc_final: 0.6308 (t0) REVERT: p 609 GLU cc_start: 0.5875 (mp0) cc_final: 0.5536 (mp0) REVERT: p 636 LYS cc_start: 0.5540 (mttt) cc_final: 0.5246 (mmtt) REVERT: p 684 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6217 (pt0) REVERT: p 728 MET cc_start: 0.6978 (mtm) cc_final: 0.6449 (mtp) REVERT: p 737 ILE cc_start: 0.7481 (mt) cc_final: 0.7272 (tp) REVERT: p 796 MET cc_start: 0.8831 (mtm) cc_final: 0.8253 (mtm) REVERT: p 817 GLN cc_start: 0.6250 (tt0) cc_final: 0.5810 (pm20) REVERT: p 850 ASP cc_start: 0.8005 (t0) cc_final: 0.7485 (p0) REVERT: p 866 ILE cc_start: 0.7578 (mt) cc_final: 0.7352 (pt) REVERT: p 958 CYS cc_start: 0.7221 (m) cc_final: 0.6893 (p) REVERT: p 959 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7404 (mt-10) REVERT: p 995 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7346 (pt0) REVERT: p 1054 MET cc_start: 0.8114 (mtm) cc_final: 0.7577 (mtt) REVERT: p 1076 GLU cc_start: 0.7810 (tt0) cc_final: 0.7227 (tm-30) REVERT: p 1080 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7154 (mtm180) REVERT: p 1115 GLN cc_start: 0.7951 (mt0) cc_final: 0.7605 (mt0) REVERT: p 1131 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7654 (mtp85) REVERT: p 1143 LYS cc_start: 0.6487 (tttp) cc_final: 0.6134 (mmtm) REVERT: p 1150 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6865 (mmm160) REVERT: p 1151 MET cc_start: 0.7715 (ptm) cc_final: 0.7293 (ptp) REVERT: p 1172 MET cc_start: 0.7142 (mmt) cc_final: 0.6357 (mmt) REVERT: q 17 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6687 (mp0) REVERT: q 81 LYS cc_start: 0.6665 (mtpt) cc_final: 0.5977 (mttt) REVERT: q 83 GLN cc_start: 0.7932 (mt0) cc_final: 0.7540 (mt0) REVERT: q 96 GLU cc_start: 0.6406 (mt-10) cc_final: 0.5868 (mp0) REVERT: q 100 GLU cc_start: 0.7603 (tt0) cc_final: 0.7297 (tt0) REVERT: q 102 THR cc_start: 0.7677 (m) cc_final: 0.7294 (p) REVERT: q 106 ARG cc_start: 0.7596 (ttt180) cc_final: 0.7000 (ttp80) REVERT: q 108 ASN cc_start: 0.7643 (m-40) cc_final: 0.7187 (p0) REVERT: q 109 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6598 (pm20) REVERT: q 121 ILE cc_start: 0.8118 (mt) cc_final: 0.7843 (mm) REVERT: q 126 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6768 (mmm-85) REVERT: q 207 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7157 (pt0) REVERT: q 215 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5957 (mt-10) REVERT: q 254 LYS cc_start: 0.6036 (tttt) cc_final: 0.5626 (mptt) REVERT: s 38 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7084 (mm-30) REVERT: s 79 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6754 (mp0) REVERT: s 91 CYS cc_start: 0.7785 (t) cc_final: 0.7232 (m) REVERT: s 121 MET cc_start: 0.7067 (ptp) cc_final: 0.6408 (pmm) REVERT: s 125 TYR cc_start: 0.6693 (m-80) cc_final: 0.6174 (m-80) REVERT: s 159 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7118 (tp) REVERT: s 197 SER cc_start: 0.8564 (t) cc_final: 0.8246 (t) REVERT: t 57 MET cc_start: 0.6965 (ttp) cc_final: 0.6505 (ttm) REVERT: t 75 MET cc_start: 0.5381 (mtt) cc_final: 0.5149 (mtp) REVERT: t 79 VAL cc_start: 0.6808 (t) cc_final: 0.6568 (t) REVERT: t 80 MET cc_start: 0.6551 (mmt) cc_final: 0.6039 (mmt) REVERT: t 98 LYS cc_start: 0.7561 (mttt) cc_final: 0.7241 (mtpt) REVERT: u 1 MET cc_start: 0.5516 (tpt) cc_final: 0.5122 (tmm) REVERT: u 2 PHE cc_start: 0.4837 (m-10) cc_final: 0.4622 (m-10) REVERT: v 21 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7834 (mmtm) REVERT: v 35 PHE cc_start: 0.7450 (m-80) cc_final: 0.7229 (m-10) REVERT: v 51 ASP cc_start: 0.7367 (m-30) cc_final: 0.6813 (t0) REVERT: v 54 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6772 (m-30) REVERT: v 63 THR cc_start: 0.8837 (p) cc_final: 0.8576 (t) REVERT: v 71 ASP cc_start: 0.6288 (m-30) cc_final: 0.5777 (m-30) REVERT: v 95 LYS cc_start: 0.6403 (tttt) cc_final: 0.6021 (ttmt) REVERT: v 100 GLU cc_start: 0.6889 (tt0) cc_final: 0.6146 (mt-10) REVERT: v 126 GLN cc_start: 0.7128 (tt0) cc_final: 0.6891 (tt0) REVERT: v 136 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6844 (mt-10) REVERT: v 138 ASP cc_start: 0.7202 (m-30) cc_final: 0.6719 (t0) REVERT: v 145 MET cc_start: 0.7953 (mtp) cc_final: 0.7655 (mtp) REVERT: v 146 LYS cc_start: 0.6531 (tttt) cc_final: 0.5999 (tttm) REVERT: w 34 ILE cc_start: 0.6012 (mt) cc_final: 0.5724 (pt) REVERT: w 56 ASN cc_start: 0.7466 (t0) cc_final: 0.7022 (t0) REVERT: w 71 ASP cc_start: 0.7658 (m-30) cc_final: 0.7224 (m-30) REVERT: w 81 THR cc_start: 0.7462 (p) cc_final: 0.7177 (t) REVERT: x 62 TYR cc_start: 0.7668 (m-80) cc_final: 0.6670 (m-80) REVERT: y 23 LYS cc_start: 0.8002 (mttt) cc_final: 0.7460 (mmtt) REVERT: y 32 LEU cc_start: 0.7226 (tp) cc_final: 0.6846 (mt) REVERT: y 47 LYS cc_start: 0.6504 (ttpp) cc_final: 0.6226 (tttm) REVERT: y 48 SER cc_start: 0.7606 (t) cc_final: 0.7315 (p) REVERT: y 70 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7216 (ttmm) REVERT: y 85 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6261 (tt0) REVERT: z 15 MET cc_start: 0.5288 (OUTLIER) cc_final: 0.4929 (ttt) REVERT: z 25 GLU cc_start: 0.7251 (mt-10) cc_final: 0.5971 (mp0) REVERT: z 35 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7521 (ttp80) REVERT: z 53 VAL cc_start: 0.8664 (t) cc_final: 0.8438 (p) outliers start: 112 outliers final: 51 residues processed: 696 average time/residue: 1.6410 time to fit residues: 1350.2865 Evaluate side-chains 615 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 554 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 48 GLU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 532 ARG Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1161 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1291 ASN Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 529 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 578 LYS Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 793 SER Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 84 ILE Chi-restraints excluded: chain s residue 87 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain x residue 55 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain y residue 52 LYS Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 0.0670 chunk 118 optimal weight: 2.9990 chunk 318 optimal weight: 50.0000 chunk 260 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 383 optimal weight: 0.2980 chunk 413 optimal weight: 1.9990 chunk 341 optimal weight: 0.7980 chunk 379 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 307 optimal weight: 4.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 576 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 904 GLN o1032 GLN o1044 HIS o1093 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 111 ASN p 117 ASN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 430 ASN p 500 GLN p 577 HIS p 650 ASN p1007 ASN ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN w 22 ASN w 45 GLN w 74 GLN w 98 GLN x 26 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5301 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36597 Z= 0.226 Angle : 0.483 10.926 49911 Z= 0.259 Chirality : 0.040 0.176 5557 Planarity : 0.003 0.062 6097 Dihedral : 16.277 177.060 5816 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.04 % Favored : 95.82 % Rotamer: Outliers : 4.04 % Allowed : 15.67 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.99 (0.13), residues: 4137 helix: 1.94 (0.14), residues: 1407 sheet: 0.26 (0.19), residues: 688 loop : -0.05 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o1192 HIS 0.023 0.001 HIS r 43 PHE 0.014 0.001 PHE q 63 TYR 0.018 0.001 TYR w 25 ARG 0.006 0.000 ARG p 975 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 577 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.7465 (mmt90) cc_final: 0.6977 (mtt-85) REVERT: o 18 ILE cc_start: 0.7582 (mt) cc_final: 0.7260 (mm) REVERT: o 58 MET cc_start: 0.7770 (ttp) cc_final: 0.7560 (ttm) REVERT: o 67 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7017 (tpp-160) REVERT: o 105 LYS cc_start: 0.5054 (OUTLIER) cc_final: 0.4767 (ttmm) REVERT: o 139 LYS cc_start: 0.5107 (ttmt) cc_final: 0.4905 (mptt) REVERT: o 192 ARG cc_start: 0.7166 (ptm160) cc_final: 0.6633 (ptt180) REVERT: o 193 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6941 (ttt180) REVERT: o 197 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6599 (pt0) REVERT: o 229 SER cc_start: 0.6274 (t) cc_final: 0.5973 (p) REVERT: o 266 MET cc_start: 0.3565 (mtm) cc_final: 0.2737 (ttp) REVERT: o 321 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6247 (mp0) REVERT: o 329 MET cc_start: 0.5480 (mpp) cc_final: 0.5115 (mmm) REVERT: o 347 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7408 (mp0) REVERT: o 411 SER cc_start: 0.7975 (m) cc_final: 0.7709 (p) REVERT: o 423 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.7139 (p0) REVERT: o 426 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6774 (mtm-85) REVERT: o 451 CYS cc_start: 0.6808 (m) cc_final: 0.6226 (p) REVERT: o 467 MET cc_start: 0.7171 (mmt) cc_final: 0.6499 (mmt) REVERT: o 473 ARG cc_start: 0.6805 (ttp-170) cc_final: 0.6152 (ttm-80) REVERT: o 532 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.6250 (ptm-80) REVERT: o 552 ASP cc_start: 0.6121 (m-30) cc_final: 0.5919 (m-30) REVERT: o 559 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6836 (mt-10) REVERT: o 561 MET cc_start: 0.7296 (mtt) cc_final: 0.6991 (mmm) REVERT: o 612 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7080 (p0) REVERT: o 691 ASP cc_start: 0.7818 (m-30) cc_final: 0.7583 (m-30) REVERT: o 728 THR cc_start: 0.7646 (m) cc_final: 0.7106 (t) REVERT: o 762 GLU cc_start: 0.7646 (mp0) cc_final: 0.7152 (mm-30) REVERT: o 796 LYS cc_start: 0.7123 (mttt) cc_final: 0.6695 (mttm) REVERT: o 803 LYS cc_start: 0.7328 (tttp) cc_final: 0.6951 (tptp) REVERT: o 818 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7267 (mp0) REVERT: o 845 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6274 (tt0) REVERT: o 868 MET cc_start: 0.7367 (ptt) cc_final: 0.7073 (ptt) REVERT: o 902 GLU cc_start: 0.6334 (tt0) cc_final: 0.5713 (mt-10) REVERT: o 937 ASP cc_start: 0.7269 (t0) cc_final: 0.6930 (m-30) REVERT: o 962 ASP cc_start: 0.6927 (m-30) cc_final: 0.6541 (m-30) REVERT: o 976 LYS cc_start: 0.7314 (ttmt) cc_final: 0.6625 (ttmt) REVERT: o 1015 GLU cc_start: 0.5663 (mt-10) cc_final: 0.5400 (mm-30) REVERT: o 1063 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6452 (pt0) REVERT: o 1085 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6368 (mt-10) REVERT: o 1133 LYS cc_start: 0.8333 (mttt) cc_final: 0.8113 (mtmm) REVERT: o 1135 LYS cc_start: 0.7265 (mttt) cc_final: 0.6942 (tppt) REVERT: o 1144 LEU cc_start: 0.7543 (tp) cc_final: 0.7285 (tm) REVERT: o 1167 ARG cc_start: 0.7056 (ttp-110) cc_final: 0.6502 (ttm-80) REVERT: o 1168 LYS cc_start: 0.8087 (mttt) cc_final: 0.7820 (mtpp) REVERT: o 1215 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6651 (tm-30) REVERT: o 1217 ASP cc_start: 0.5782 (t0) cc_final: 0.5440 (t0) REVERT: o 1262 MET cc_start: 0.6642 (ttt) cc_final: 0.6330 (tpp) REVERT: o 1281 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6793 (t0) REVERT: o 1302 GLU cc_start: 0.7343 (pt0) cc_final: 0.6759 (mp0) REVERT: o 1303 GLN cc_start: 0.7947 (mt0) cc_final: 0.7614 (mp10) REVERT: o 1306 LYS cc_start: 0.5873 (mttt) cc_final: 0.5237 (mmmt) REVERT: o 1311 LEU cc_start: 0.8491 (mt) cc_final: 0.8270 (mt) REVERT: o 1334 TRP cc_start: 0.8774 (m100) cc_final: 0.8429 (m100) REVERT: o 1337 GLU cc_start: 0.6338 (mt-10) cc_final: 0.6031 (mm-30) REVERT: o 1344 MET cc_start: 0.6475 (tpp) cc_final: 0.6210 (tpt) REVERT: o 1351 ASP cc_start: 0.7889 (m-30) cc_final: 0.7587 (m-30) REVERT: o 1421 ARG cc_start: 0.7138 (mmt-90) cc_final: 0.6866 (mmp-170) REVERT: o 1422 GLN cc_start: 0.6817 (mt0) cc_final: 0.6083 (mm110) REVERT: o 1452 LYS cc_start: 0.6933 (mttt) cc_final: 0.6608 (mmtt) REVERT: p 17 ILE cc_start: 0.8118 (mt) cc_final: 0.7699 (mm) REVERT: p 117 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.7041 (m-40) REVERT: p 144 HIS cc_start: 0.7009 (m90) cc_final: 0.6620 (m170) REVERT: p 160 TYR cc_start: 0.7334 (m-80) cc_final: 0.6999 (m-80) REVERT: p 200 MET cc_start: 0.8017 (ttm) cc_final: 0.7478 (ttm) REVERT: p 215 TYR cc_start: 0.6992 (m-80) cc_final: 0.5961 (m-80) REVERT: p 239 MET cc_start: 0.6726 (ttm) cc_final: 0.6275 (ttp) REVERT: p 307 GLU cc_start: 0.8427 (tp30) cc_final: 0.8193 (tp30) REVERT: p 312 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6411 (tm-30) REVERT: p 358 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6616 (pm20) REVERT: p 516 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: p 546 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6549 (mt-10) REVERT: p 563 ASP cc_start: 0.3737 (m-30) cc_final: 0.3442 (m-30) REVERT: p 591 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5359 (ttt180) REVERT: p 597 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7173 (mm) REVERT: p 606 ASP cc_start: 0.6579 (t0) cc_final: 0.6286 (t0) REVERT: p 637 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7341 (mtmm) REVERT: p 684 GLU cc_start: 0.6454 (mt-10) cc_final: 0.5869 (mm-30) REVERT: p 728 MET cc_start: 0.6998 (mtm) cc_final: 0.6370 (mtp) REVERT: p 786 THR cc_start: 0.7919 (OUTLIER) cc_final: 0.7672 (p) REVERT: p 796 MET cc_start: 0.8978 (mtm) cc_final: 0.8474 (mtm) REVERT: p 817 GLN cc_start: 0.6207 (tt0) cc_final: 0.5670 (pm20) REVERT: p 850 ASP cc_start: 0.8068 (t0) cc_final: 0.7547 (p0) REVERT: p 866 ILE cc_start: 0.7342 (mt) cc_final: 0.6995 (pt) REVERT: p 895 PHE cc_start: 0.7579 (m-80) cc_final: 0.7193 (m-80) REVERT: p 916 TYR cc_start: 0.6600 (m-10) cc_final: 0.6196 (m-80) REVERT: p 958 CYS cc_start: 0.7551 (m) cc_final: 0.7200 (p) REVERT: p 995 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7344 (pt0) REVERT: p 1054 MET cc_start: 0.8160 (mtm) cc_final: 0.7818 (mtt) REVERT: p 1076 GLU cc_start: 0.7831 (tt0) cc_final: 0.7322 (tm-30) REVERT: p 1080 ARG cc_start: 0.7603 (mtt90) cc_final: 0.7300 (mtm180) REVERT: p 1115 GLN cc_start: 0.7982 (mt0) cc_final: 0.7637 (mt0) REVERT: p 1143 LYS cc_start: 0.6524 (tttp) cc_final: 0.6192 (mmtm) REVERT: p 1150 ARG cc_start: 0.7267 (mtt180) cc_final: 0.7024 (mmm160) REVERT: p 1151 MET cc_start: 0.7802 (ptm) cc_final: 0.7394 (ptp) REVERT: p 1172 MET cc_start: 0.7141 (mmt) cc_final: 0.6590 (mmt) REVERT: q 17 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6635 (mp0) REVERT: q 81 LYS cc_start: 0.7010 (mtpt) cc_final: 0.6227 (mttt) REVERT: q 83 GLN cc_start: 0.7836 (mt0) cc_final: 0.7464 (mt0) REVERT: q 96 GLU cc_start: 0.6511 (mt-10) cc_final: 0.5890 (mp0) REVERT: q 100 GLU cc_start: 0.7725 (tt0) cc_final: 0.7438 (tt0) REVERT: q 102 THR cc_start: 0.7631 (m) cc_final: 0.7156 (p) REVERT: q 106 ARG cc_start: 0.7843 (ttt180) cc_final: 0.7505 (ttp80) REVERT: q 108 ASN cc_start: 0.7650 (m-40) cc_final: 0.7198 (p0) REVERT: q 109 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6755 (pm20) REVERT: q 121 ILE cc_start: 0.7746 (mt) cc_final: 0.7463 (mm) REVERT: q 126 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6850 (mmm-85) REVERT: q 207 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7161 (pt0) REVERT: q 215 GLU cc_start: 0.6277 (mt-10) cc_final: 0.5802 (mt-10) REVERT: q 254 LYS cc_start: 0.5985 (tttt) cc_final: 0.5585 (mptt) REVERT: r 39 MET cc_start: 0.8783 (ptt) cc_final: 0.8529 (ppp) REVERT: s 26 TYR cc_start: 0.7284 (m-80) cc_final: 0.6562 (m-80) REVERT: s 38 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7073 (mm-30) REVERT: s 79 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6774 (mp0) REVERT: s 96 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: s 99 ILE cc_start: 0.8397 (mt) cc_final: 0.7917 (mm) REVERT: s 125 TYR cc_start: 0.6832 (m-80) cc_final: 0.6625 (m-80) REVERT: s 159 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7476 (tp) REVERT: s 197 SER cc_start: 0.8587 (t) cc_final: 0.8276 (t) REVERT: s 210 GLN cc_start: 0.6485 (mt0) cc_final: 0.6152 (tm-30) REVERT: t 57 MET cc_start: 0.7092 (ttp) cc_final: 0.6600 (ttm) REVERT: t 80 MET cc_start: 0.6405 (mmt) cc_final: 0.5987 (mmt) REVERT: t 86 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6264 (mm-30) REVERT: u 44 PHE cc_start: 0.7646 (m-80) cc_final: 0.7153 (m-10) REVERT: v 21 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7816 (mmtm) REVERT: v 36 LYS cc_start: 0.6566 (mmtt) cc_final: 0.6239 (mmpt) REVERT: v 51 ASP cc_start: 0.7589 (m-30) cc_final: 0.7176 (t0) REVERT: v 63 THR cc_start: 0.8807 (p) cc_final: 0.8546 (t) REVERT: v 71 ASP cc_start: 0.6154 (m-30) cc_final: 0.5625 (m-30) REVERT: v 95 LYS cc_start: 0.6831 (tttt) cc_final: 0.6356 (ttmt) REVERT: v 100 GLU cc_start: 0.6955 (tt0) cc_final: 0.6197 (mt-10) REVERT: v 126 GLN cc_start: 0.7083 (tt0) cc_final: 0.6837 (tt0) REVERT: v 136 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6683 (mt-10) REVERT: v 138 ASP cc_start: 0.7282 (m-30) cc_final: 0.6740 (t0) REVERT: v 146 LYS cc_start: 0.6461 (tttt) cc_final: 0.5921 (tttm) REVERT: w 23 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7807 (ttt) REVERT: w 56 ASN cc_start: 0.7362 (t0) cc_final: 0.6871 (t0) REVERT: w 68 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6985 (mp) REVERT: w 71 ASP cc_start: 0.7892 (m-30) cc_final: 0.7421 (m-30) REVERT: x 13 ILE cc_start: 0.8690 (mm) cc_final: 0.8431 (mp) REVERT: x 19 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: y 23 LYS cc_start: 0.7983 (mttt) cc_final: 0.7444 (mmmt) REVERT: y 47 LYS cc_start: 0.6329 (ttpp) cc_final: 0.6076 (tttm) REVERT: y 48 SER cc_start: 0.7683 (t) cc_final: 0.7364 (p) REVERT: y 55 GLN cc_start: 0.8004 (mt0) cc_final: 0.7687 (mt0) REVERT: y 70 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7136 (ttmm) REVERT: z 15 MET cc_start: 0.5477 (OUTLIER) cc_final: 0.5038 (ttt) REVERT: z 25 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6099 (mp0) REVERT: z 53 VAL cc_start: 0.8695 (t) cc_final: 0.8481 (p) outliers start: 149 outliers final: 59 residues processed: 659 average time/residue: 1.7051 time to fit residues: 1340.1142 Evaluate side-chains 610 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 532 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 325 LEU Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 532 ARG Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1139 LEU Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1161 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1367 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 117 ASN Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 793 SER Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 87 ILE Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 0.5980 chunk 287 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 chunk 406 optimal weight: 0.0870 chunk 200 optimal weight: 2.9990 chunk 364 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 22 GLN o 62 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS o1410 HIS p 145 GLN p 265 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 430 ASN p 500 GLN p 749 HIS p 980 HIS ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 76 ASN w 22 ASN w 45 GLN w 98 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5319 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36597 Z= 0.229 Angle : 0.467 9.993 49911 Z= 0.250 Chirality : 0.040 0.158 5557 Planarity : 0.003 0.056 6097 Dihedral : 16.132 179.515 5809 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.33 % Favored : 95.53 % Rotamer: Outliers : 3.80 % Allowed : 16.95 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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 (0.13), residues: 4137 helix: 1.98 (0.14), residues: 1409 sheet: 0.26 (0.20), residues: 675 loop : -0.09 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o1192 HIS 0.015 0.001 HIS r 43 PHE 0.015 0.001 PHE q 63 TYR 0.012 0.001 TYR p 160 ARG 0.007 0.000 ARG o1149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 559 time to evaluate : 4.101 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: o 16 ARG cc_start: 0.7505 (mmt90) cc_final: 0.7054 (mtt-85) REVERT: o 18 ILE cc_start: 0.7647 (mt) cc_final: 0.7400 (mm) REVERT: o 34 MET cc_start: 0.7605 (ptm) cc_final: 0.7401 (ptt) REVERT: o 58 MET cc_start: 0.7783 (ttp) cc_final: 0.7568 (ttm) REVERT: o 67 ARG cc_start: 0.8100 (ttp80) cc_final: 0.6933 (tpp-160) REVERT: o 103 THR cc_start: 0.7658 (m) cc_final: 0.7423 (m) REVERT: o 105 LYS cc_start: 0.5162 (OUTLIER) cc_final: 0.4952 (ttmm) REVERT: o 192 ARG cc_start: 0.7099 (ptm160) cc_final: 0.6654 (ptt180) REVERT: o 193 ARG cc_start: 0.7261 (ttp80) cc_final: 0.6972 (ttt180) REVERT: o 194 SER cc_start: 0.7294 (t) cc_final: 0.7053 (p) REVERT: o 197 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7089 (mt-10) REVERT: o 229 SER cc_start: 0.6389 (t) cc_final: 0.5946 (p) REVERT: o 246 GLU cc_start: 0.7025 (pt0) cc_final: 0.6644 (pm20) REVERT: o 266 MET cc_start: 0.3618 (mtm) cc_final: 0.2751 (ttp) REVERT: o 321 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6168 (mp0) REVERT: o 329 MET cc_start: 0.5362 (mpp) cc_final: 0.5045 (mmm) REVERT: o 411 SER cc_start: 0.7994 (m) cc_final: 0.7707 (p) REVERT: o 423 ASN cc_start: 0.7582 (OUTLIER) cc_final: 0.7196 (p0) REVERT: o 451 CYS cc_start: 0.6856 (m) cc_final: 0.6269 (p) REVERT: o 473 ARG cc_start: 0.6874 (ttp-170) cc_final: 0.6250 (ttm-80) REVERT: o 552 ASP cc_start: 0.6189 (m-30) cc_final: 0.5989 (m-30) REVERT: o 559 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6755 (mt-10) REVERT: o 561 MET cc_start: 0.7297 (mtt) cc_final: 0.7018 (mmm) REVERT: o 612 ASP cc_start: 0.7499 (m-30) cc_final: 0.7090 (p0) REVERT: o 673 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7236 (mt0) REVERT: o 691 ASP cc_start: 0.7885 (m-30) cc_final: 0.7653 (m-30) REVERT: o 728 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.6992 (t) REVERT: o 761 SER cc_start: 0.7147 (m) cc_final: 0.6590 (t) REVERT: o 762 GLU cc_start: 0.7640 (mp0) cc_final: 0.7183 (mm-30) REVERT: o 796 LYS cc_start: 0.7180 (mttt) cc_final: 0.6724 (mttm) REVERT: o 803 LYS cc_start: 0.7330 (tttp) cc_final: 0.6922 (tptt) REVERT: o 818 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7250 (mp0) REVERT: o 845 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6303 (tt0) REVERT: o 868 MET cc_start: 0.7324 (ptt) cc_final: 0.7046 (ptt) REVERT: o 902 GLU cc_start: 0.6334 (tt0) cc_final: 0.5658 (mt-10) REVERT: o 960 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.4796 (ttm-80) REVERT: o 962 ASP cc_start: 0.6950 (m-30) cc_final: 0.6412 (m-30) REVERT: o 976 LYS cc_start: 0.7336 (ttmt) cc_final: 0.6577 (ttmt) REVERT: o 1063 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6667 (pt0) REVERT: o 1085 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6253 (mt-10) REVERT: o 1133 LYS cc_start: 0.8351 (mttt) cc_final: 0.8149 (mtmm) REVERT: o 1135 LYS cc_start: 0.7190 (mttt) cc_final: 0.6845 (tppt) REVERT: o 1144 LEU cc_start: 0.7734 (tp) cc_final: 0.7492 (tm) REVERT: o 1167 ARG cc_start: 0.7154 (ttp-110) cc_final: 0.6500 (ttm-80) REVERT: o 1215 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6570 (tm-30) REVERT: o 1219 LYS cc_start: 0.7732 (tptt) cc_final: 0.7332 (tmtt) REVERT: o 1262 MET cc_start: 0.6697 (ttt) cc_final: 0.6398 (tpp) REVERT: o 1281 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6916 (t0) REVERT: o 1302 GLU cc_start: 0.7379 (pt0) cc_final: 0.6803 (mp0) REVERT: o 1303 GLN cc_start: 0.7886 (mt0) cc_final: 0.7558 (mp10) REVERT: o 1306 LYS cc_start: 0.5903 (mttt) cc_final: 0.5260 (mmmt) REVERT: o 1337 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6118 (mm-30) REVERT: o 1344 MET cc_start: 0.6587 (tpp) cc_final: 0.6369 (tpt) REVERT: o 1351 ASP cc_start: 0.7958 (m-30) cc_final: 0.7654 (m-30) REVERT: o 1422 GLN cc_start: 0.6771 (mt0) cc_final: 0.6064 (mm110) REVERT: o 1452 LYS cc_start: 0.7001 (mttt) cc_final: 0.6648 (mmtt) REVERT: p 17 ILE cc_start: 0.8218 (mt) cc_final: 0.7813 (mm) REVERT: p 144 HIS cc_start: 0.7090 (m90) cc_final: 0.6721 (m170) REVERT: p 160 TYR cc_start: 0.7327 (m-80) cc_final: 0.6997 (m-80) REVERT: p 200 MET cc_start: 0.8061 (ttm) cc_final: 0.7475 (ttm) REVERT: p 222 ARG cc_start: 0.6402 (mtm180) cc_final: 0.5844 (mtp85) REVERT: p 239 MET cc_start: 0.6765 (ttm) cc_final: 0.6327 (ttp) REVERT: p 307 GLU cc_start: 0.8401 (tp30) cc_final: 0.8172 (tp30) REVERT: p 309 PHE cc_start: 0.8566 (t80) cc_final: 0.8362 (t80) REVERT: p 312 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6606 (tm-30) REVERT: p 358 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6643 (pm20) REVERT: p 516 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: p 546 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6683 (mt-10) REVERT: p 578 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7230 (mptp) REVERT: p 597 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7304 (mm) REVERT: p 606 ASP cc_start: 0.6671 (t0) cc_final: 0.6284 (t0) REVERT: p 609 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5439 (mp0) REVERT: p 637 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7320 (mtmm) REVERT: p 684 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6294 (mm-30) REVERT: p 728 MET cc_start: 0.7113 (mtm) cc_final: 0.6537 (mtp) REVERT: p 786 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7795 (p) REVERT: p 796 MET cc_start: 0.9020 (mtm) cc_final: 0.8303 (ttt) REVERT: p 798 ARG cc_start: 0.6774 (ttt90) cc_final: 0.6493 (tpt90) REVERT: p 817 GLN cc_start: 0.6102 (tt0) cc_final: 0.5710 (pm20) REVERT: p 850 ASP cc_start: 0.8065 (t0) cc_final: 0.7531 (p0) REVERT: p 866 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.7002 (pt) REVERT: p 916 TYR cc_start: 0.6507 (m-10) cc_final: 0.6237 (m-80) REVERT: p 958 CYS cc_start: 0.7610 (m) cc_final: 0.7291 (p) REVERT: p 995 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7346 (pt0) REVERT: p 1076 GLU cc_start: 0.7824 (tt0) cc_final: 0.7356 (tm-30) REVERT: p 1080 ARG cc_start: 0.7469 (mtt90) cc_final: 0.7214 (mtm180) REVERT: p 1151 MET cc_start: 0.7925 (ptm) cc_final: 0.7540 (ptp) REVERT: p 1172 MET cc_start: 0.7215 (mmt) cc_final: 0.6632 (mmt) REVERT: q 17 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6627 (mt-10) REVERT: q 44 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6245 (tp) REVERT: q 81 LYS cc_start: 0.7026 (mtpt) cc_final: 0.6195 (mttt) REVERT: q 83 GLN cc_start: 0.7750 (mt0) cc_final: 0.7360 (mt0) REVERT: q 96 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6372 (mp0) REVERT: q 100 GLU cc_start: 0.7727 (tt0) cc_final: 0.7444 (tt0) REVERT: q 102 THR cc_start: 0.7408 (m) cc_final: 0.7080 (p) REVERT: q 106 ARG cc_start: 0.7964 (ttt180) cc_final: 0.7709 (ttp80) REVERT: q 108 ASN cc_start: 0.7675 (m-40) cc_final: 0.7156 (p0) REVERT: q 109 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6805 (pm20) REVERT: q 121 ILE cc_start: 0.7684 (mt) cc_final: 0.7432 (mm) REVERT: q 126 ARG cc_start: 0.7493 (mtt180) cc_final: 0.6850 (mmm-85) REVERT: q 207 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7096 (pt0) REVERT: q 215 GLU cc_start: 0.6266 (mt-10) cc_final: 0.5753 (mt-10) REVERT: q 254 LYS cc_start: 0.5983 (tttt) cc_final: 0.5571 (mptt) REVERT: r 39 MET cc_start: 0.8562 (ptt) cc_final: 0.8321 (mmm) REVERT: s 4 GLU cc_start: 0.6966 (tp30) cc_final: 0.6558 (tp30) REVERT: s 26 TYR cc_start: 0.7340 (m-80) cc_final: 0.6777 (m-80) REVERT: s 38 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7076 (mm-30) REVERT: s 61 LEU cc_start: 0.8059 (tp) cc_final: 0.7581 (tm) REVERT: s 79 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6793 (mp0) REVERT: s 99 ILE cc_start: 0.8485 (mt) cc_final: 0.7885 (mm) REVERT: s 116 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6684 (tp40) REVERT: s 125 TYR cc_start: 0.6954 (m-80) cc_final: 0.6721 (m-80) REVERT: s 159 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7517 (tp) REVERT: s 197 SER cc_start: 0.8538 (t) cc_final: 0.8229 (t) REVERT: s 210 GLN cc_start: 0.6505 (mt0) cc_final: 0.6180 (tm-30) REVERT: t 57 MET cc_start: 0.7016 (ttp) cc_final: 0.6639 (ttm) REVERT: t 80 MET cc_start: 0.6363 (mmt) cc_final: 0.6016 (mmt) REVERT: t 86 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6338 (mm-30) REVERT: u 157 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6267 (tp) REVERT: v 36 LYS cc_start: 0.6612 (mmtt) cc_final: 0.6351 (mmpt) REVERT: v 51 ASP cc_start: 0.7565 (m-30) cc_final: 0.7168 (t0) REVERT: v 63 THR cc_start: 0.8808 (p) cc_final: 0.8543 (t) REVERT: v 71 ASP cc_start: 0.6170 (m-30) cc_final: 0.5654 (m-30) REVERT: v 95 LYS cc_start: 0.6634 (tttt) cc_final: 0.6301 (ttmt) REVERT: v 100 GLU cc_start: 0.6925 (tt0) cc_final: 0.6239 (mt-10) REVERT: v 133 HIS cc_start: 0.7374 (p-80) cc_final: 0.6323 (m170) REVERT: v 136 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6680 (mt-10) REVERT: v 145 MET cc_start: 0.7849 (mtp) cc_final: 0.7621 (mtp) REVERT: v 146 LYS cc_start: 0.6423 (tttt) cc_final: 0.5922 (tttm) REVERT: w 23 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7823 (ttt) REVERT: w 56 ASN cc_start: 0.7087 (t0) cc_final: 0.6480 (t0) REVERT: w 68 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7064 (mp) REVERT: w 71 ASP cc_start: 0.7945 (m-30) cc_final: 0.7464 (m-30) REVERT: x 13 ILE cc_start: 0.8722 (mm) cc_final: 0.8450 (mp) REVERT: x 19 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: x 26 GLN cc_start: 0.7951 (tt0) cc_final: 0.7582 (tm-30) REVERT: y 16 GLU cc_start: 0.6552 (tt0) cc_final: 0.6290 (mt-10) REVERT: y 23 LYS cc_start: 0.8038 (mttt) cc_final: 0.7458 (mmmt) REVERT: y 38 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.5914 (mp0) REVERT: y 47 LYS cc_start: 0.6293 (ttpp) cc_final: 0.6037 (tttm) REVERT: y 48 SER cc_start: 0.7741 (t) cc_final: 0.7399 (p) REVERT: y 55 GLN cc_start: 0.8060 (mt0) cc_final: 0.7712 (mt0) REVERT: y 70 LYS cc_start: 0.7856 (ttpt) cc_final: 0.7239 (ttmm) REVERT: z 15 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.5123 (ttt) REVERT: z 25 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6155 (mp0) REVERT: z 35 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7523 (ttm110) outliers start: 140 outliers final: 73 residues processed: 641 average time/residue: 1.6144 time to fit residues: 1229.6588 Evaluate side-chains 628 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 532 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 673 GLN Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 828 LEU Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 220 GLU Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 417 ILE Chi-restraints excluded: chain p residue 423 ILE Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 578 LYS Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 861 SER Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 896 LEU Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 157 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 50 LYS Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 0.0000 chunk 231 optimal weight: 0.9990 chunk 5 optimal weight: 50.0000 chunk 302 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 chunk 347 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 365 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 353 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 576 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 945 ASN o1163 HIS o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 430 ASN p 500 GLN p 518 HIS ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1115 GLN p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 76 ASN w 22 ASN w 98 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5312 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36597 Z= 0.162 Angle : 0.429 9.891 49911 Z= 0.230 Chirality : 0.039 0.163 5557 Planarity : 0.003 0.048 6097 Dihedral : 15.972 177.580 5809 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.13 % Favored : 95.72 % Rotamer: Outliers : 3.61 % Allowed : 17.49 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 1.18 (0.13), residues: 4137 helix: 2.23 (0.14), residues: 1404 sheet: 0.37 (0.20), residues: 661 loop : -0.02 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o1192 HIS 0.014 0.001 HIS r 43 PHE 0.012 0.001 PHE q 63 TYR 0.009 0.001 TYR o1197 ARG 0.005 0.000 ARG p 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 563 time to evaluate : 3.473 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: o 16 ARG cc_start: 0.7475 (mmt90) cc_final: 0.7132 (mtt-85) REVERT: o 18 ILE cc_start: 0.7681 (mt) cc_final: 0.7435 (mm) REVERT: o 58 MET cc_start: 0.7760 (ttp) cc_final: 0.7545 (ttm) REVERT: o 67 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7052 (tpp-160) REVERT: o 105 LYS cc_start: 0.5133 (OUTLIER) cc_final: 0.4878 (ttmm) REVERT: o 140 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5399 (ttp80) REVERT: o 149 LYS cc_start: 0.7774 (ptpp) cc_final: 0.7534 (ptpp) REVERT: o 192 ARG cc_start: 0.7011 (ptm160) cc_final: 0.6725 (ptt180) REVERT: o 229 SER cc_start: 0.6395 (t) cc_final: 0.5956 (p) REVERT: o 234 PHE cc_start: 0.7458 (t80) cc_final: 0.7186 (t80) REVERT: o 246 GLU cc_start: 0.7041 (pt0) cc_final: 0.6807 (pm20) REVERT: o 266 MET cc_start: 0.3674 (mtm) cc_final: 0.2801 (ttp) REVERT: o 321 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6084 (mp0) REVERT: o 329 MET cc_start: 0.5384 (mpp) cc_final: 0.5029 (mmm) REVERT: o 347 GLU cc_start: 0.7121 (mp0) cc_final: 0.6919 (mp0) REVERT: o 411 SER cc_start: 0.7998 (m) cc_final: 0.7698 (p) REVERT: o 423 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7335 (p0) REVERT: o 451 CYS cc_start: 0.6896 (m) cc_final: 0.6308 (p) REVERT: o 473 ARG cc_start: 0.6818 (ttp-170) cc_final: 0.6136 (ttm-80) REVERT: o 495 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.6145 (p0) REVERT: o 552 ASP cc_start: 0.6146 (m-30) cc_final: 0.5865 (m-30) REVERT: o 559 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6752 (mt-10) REVERT: o 561 MET cc_start: 0.7264 (mtt) cc_final: 0.7002 (mmm) REVERT: o 612 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7143 (p0) REVERT: o 637 MET cc_start: 0.8180 (ptm) cc_final: 0.7978 (ptt) REVERT: o 683 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.5605 (tp30) REVERT: o 691 ASP cc_start: 0.7782 (m-30) cc_final: 0.7542 (m-30) REVERT: o 728 THR cc_start: 0.7625 (OUTLIER) cc_final: 0.7023 (t) REVERT: o 761 SER cc_start: 0.7028 (m) cc_final: 0.6741 (t) REVERT: o 762 GLU cc_start: 0.7625 (mp0) cc_final: 0.7192 (mm-30) REVERT: o 796 LYS cc_start: 0.7197 (mttt) cc_final: 0.6760 (mttm) REVERT: o 803 LYS cc_start: 0.7477 (tttp) cc_final: 0.6879 (tptt) REVERT: o 818 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7307 (mp0) REVERT: o 845 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6167 (tt0) REVERT: o 868 MET cc_start: 0.7307 (ptt) cc_final: 0.7072 (ptt) REVERT: o 902 GLU cc_start: 0.6357 (tt0) cc_final: 0.5719 (mt-10) REVERT: o 937 ASP cc_start: 0.7319 (t0) cc_final: 0.6992 (m-30) REVERT: o 960 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.4934 (ttm-80) REVERT: o 962 ASP cc_start: 0.6959 (m-30) cc_final: 0.6393 (m-30) REVERT: o 976 LYS cc_start: 0.7350 (ttmt) cc_final: 0.6597 (ttmt) REVERT: o 1063 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6504 (pt0) REVERT: o 1085 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6204 (tp30) REVERT: o 1133 LYS cc_start: 0.8385 (mttt) cc_final: 0.8180 (mtmm) REVERT: o 1135 LYS cc_start: 0.7246 (mttt) cc_final: 0.6940 (tppt) REVERT: o 1144 LEU cc_start: 0.7771 (tp) cc_final: 0.7547 (tm) REVERT: o 1167 ARG cc_start: 0.7114 (ttp-110) cc_final: 0.6362 (ttm-80) REVERT: o 1215 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6755 (tm-30) REVERT: o 1262 MET cc_start: 0.6880 (ttt) cc_final: 0.6474 (tpp) REVERT: o 1279 MET cc_start: 0.5869 (ttp) cc_final: 0.5581 (ttp) REVERT: o 1281 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6846 (t0) REVERT: o 1284 PHE cc_start: 0.7347 (t80) cc_final: 0.7041 (t80) REVERT: o 1302 GLU cc_start: 0.7367 (pt0) cc_final: 0.6804 (mp0) REVERT: o 1303 GLN cc_start: 0.7881 (mt0) cc_final: 0.7528 (mp10) REVERT: o 1306 LYS cc_start: 0.5788 (mttt) cc_final: 0.5111 (mmmt) REVERT: o 1329 LYS cc_start: 0.7366 (tttt) cc_final: 0.7046 (tttp) REVERT: o 1337 GLU cc_start: 0.6462 (mt-10) cc_final: 0.6101 (mm-30) REVERT: o 1344 MET cc_start: 0.6549 (tpp) cc_final: 0.6320 (tpt) REVERT: o 1351 ASP cc_start: 0.7821 (m-30) cc_final: 0.7513 (m-30) REVERT: o 1422 GLN cc_start: 0.6861 (mt0) cc_final: 0.6106 (mm110) REVERT: o 1452 LYS cc_start: 0.7025 (mttt) cc_final: 0.6646 (mmtt) REVERT: p 17 ILE cc_start: 0.8223 (mt) cc_final: 0.7894 (mm) REVERT: p 144 HIS cc_start: 0.6921 (m90) cc_final: 0.6548 (m170) REVERT: p 160 TYR cc_start: 0.7274 (m-80) cc_final: 0.6940 (m-80) REVERT: p 200 MET cc_start: 0.8046 (ttm) cc_final: 0.7524 (ttm) REVERT: p 222 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6051 (mtp85) REVERT: p 239 MET cc_start: 0.6759 (ttm) cc_final: 0.6345 (ttp) REVERT: p 307 GLU cc_start: 0.8393 (tp30) cc_final: 0.8166 (tp30) REVERT: p 309 PHE cc_start: 0.8581 (t80) cc_final: 0.8307 (t80) REVERT: p 312 GLN cc_start: 0.7135 (tm-30) cc_final: 0.6653 (tm-30) REVERT: p 358 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6608 (pm20) REVERT: p 516 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: p 546 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6807 (mt-10) REVERT: p 578 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7555 (mptp) REVERT: p 593 GLN cc_start: 0.5864 (mm-40) cc_final: 0.5396 (mt0) REVERT: p 597 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7917 (mp) REVERT: p 606 ASP cc_start: 0.6663 (t0) cc_final: 0.6366 (t0) REVERT: p 637 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7294 (mtmm) REVERT: p 684 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6323 (mm-30) REVERT: p 728 MET cc_start: 0.6990 (mtm) cc_final: 0.6432 (mtp) REVERT: p 786 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7870 (p) REVERT: p 796 MET cc_start: 0.9001 (mtm) cc_final: 0.8289 (ttt) REVERT: p 798 ARG cc_start: 0.6814 (ttt90) cc_final: 0.6537 (tpt90) REVERT: p 817 GLN cc_start: 0.6312 (tt0) cc_final: 0.5705 (pm20) REVERT: p 827 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7522 (mt-10) REVERT: p 850 ASP cc_start: 0.8130 (t0) cc_final: 0.7675 (p0) REVERT: p 866 ILE cc_start: 0.7175 (mt) cc_final: 0.6784 (pt) REVERT: p 916 TYR cc_start: 0.6549 (m-10) cc_final: 0.6147 (m-80) REVERT: p 958 CYS cc_start: 0.7603 (m) cc_final: 0.7355 (p) REVERT: p 976 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: p 995 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7196 (pt0) REVERT: p 1072 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6003 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7877 (tt0) cc_final: 0.7443 (tm-30) REVERT: p 1080 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7187 (mtm180) REVERT: p 1151 MET cc_start: 0.7939 (ptm) cc_final: 0.7567 (ptp) REVERT: p 1172 MET cc_start: 0.7193 (mmt) cc_final: 0.6619 (mmt) REVERT: q 17 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6598 (mt-10) REVERT: q 41 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: q 81 LYS cc_start: 0.7316 (mtpt) cc_final: 0.6482 (mttt) REVERT: q 83 GLN cc_start: 0.7718 (mt0) cc_final: 0.7467 (mt0) REVERT: q 96 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6382 (mp0) REVERT: q 100 GLU cc_start: 0.7702 (tt0) cc_final: 0.7434 (tt0) REVERT: q 102 THR cc_start: 0.7338 (m) cc_final: 0.6994 (p) REVERT: q 106 ARG cc_start: 0.8007 (ttt180) cc_final: 0.7626 (ttp80) REVERT: q 108 ASN cc_start: 0.7726 (m-40) cc_final: 0.7199 (p0) REVERT: q 109 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6780 (pm20) REVERT: q 118 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7243 (ttm170) REVERT: q 121 ILE cc_start: 0.7484 (mt) cc_final: 0.7253 (mm) REVERT: q 126 ARG cc_start: 0.7615 (mtt180) cc_final: 0.6892 (mmm-85) REVERT: q 207 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: q 215 GLU cc_start: 0.6259 (mt-10) cc_final: 0.5929 (mt-10) REVERT: q 254 LYS cc_start: 0.6041 (tttt) cc_final: 0.5637 (mptt) REVERT: s 3 ASP cc_start: 0.6462 (m-30) cc_final: 0.6244 (m-30) REVERT: s 26 TYR cc_start: 0.7283 (m-80) cc_final: 0.6728 (m-80) REVERT: s 38 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7111 (mm-30) REVERT: s 61 LEU cc_start: 0.8104 (tp) cc_final: 0.7581 (tm) REVERT: s 71 GLN cc_start: 0.7295 (mt0) cc_final: 0.7079 (mt0) REVERT: s 79 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6817 (mp0) REVERT: s 121 MET cc_start: 0.7230 (ptp) cc_final: 0.6663 (pmm) REVERT: s 125 TYR cc_start: 0.6881 (m-80) cc_final: 0.6580 (m-80) REVERT: s 159 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7466 (tp) REVERT: s 187 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6346 (mtp85) REVERT: s 197 SER cc_start: 0.8478 (t) cc_final: 0.8170 (t) REVERT: s 210 GLN cc_start: 0.6581 (mt0) cc_final: 0.6319 (tp40) REVERT: t 57 MET cc_start: 0.6973 (ttp) cc_final: 0.6619 (ttm) REVERT: t 80 MET cc_start: 0.6331 (mmt) cc_final: 0.6004 (mmt) REVERT: t 86 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6530 (mm-30) REVERT: v 36 LYS cc_start: 0.6556 (mmtt) cc_final: 0.6313 (mmpt) REVERT: v 51 ASP cc_start: 0.7564 (m-30) cc_final: 0.7206 (t0) REVERT: v 55 LYS cc_start: 0.7396 (mtmt) cc_final: 0.6887 (ttmm) REVERT: v 63 THR cc_start: 0.8789 (p) cc_final: 0.8535 (t) REVERT: v 71 ASP cc_start: 0.6203 (m-30) cc_final: 0.5686 (m-30) REVERT: v 87 GLN cc_start: 0.7301 (mp10) cc_final: 0.6934 (mm-40) REVERT: v 95 LYS cc_start: 0.6557 (tttt) cc_final: 0.6236 (ttmt) REVERT: v 100 GLU cc_start: 0.6934 (tt0) cc_final: 0.6251 (mt-10) REVERT: v 133 HIS cc_start: 0.7481 (p-80) cc_final: 0.6504 (m170) REVERT: v 136 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6605 (mt-10) REVERT: v 146 LYS cc_start: 0.6431 (tttt) cc_final: 0.5926 (tttm) REVERT: w 23 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8059 (ttt) REVERT: w 56 ASN cc_start: 0.6918 (t0) cc_final: 0.6371 (t0) REVERT: w 68 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7040 (mp) REVERT: w 71 ASP cc_start: 0.7940 (m-30) cc_final: 0.7560 (m-30) REVERT: w 109 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7846 (ptm160) REVERT: x 13 ILE cc_start: 0.8745 (mm) cc_final: 0.8462 (mp) REVERT: x 19 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: x 26 GLN cc_start: 0.7865 (tt0) cc_final: 0.7566 (tm-30) REVERT: y 23 LYS cc_start: 0.8086 (mttt) cc_final: 0.7520 (mmmt) REVERT: y 38 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.5874 (mp0) REVERT: y 47 LYS cc_start: 0.6242 (ttpp) cc_final: 0.5969 (tttm) REVERT: y 48 SER cc_start: 0.7736 (t) cc_final: 0.7407 (p) REVERT: y 55 GLN cc_start: 0.8030 (mt0) cc_final: 0.7605 (mt0) REVERT: y 70 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7291 (ttmm) REVERT: z 15 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.5366 (ttt) REVERT: z 21 GLU cc_start: 0.7035 (tt0) cc_final: 0.6632 (tt0) REVERT: z 25 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6086 (mp0) REVERT: z 35 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7660 (ttp80) outliers start: 133 outliers final: 59 residues processed: 642 average time/residue: 1.6152 time to fit residues: 1234.2264 Evaluate side-chains 625 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 538 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 140 ARG Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 828 LEU Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 220 GLU Chi-restraints excluded: chain p residue 222 ARG Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 423 ILE Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 578 LYS Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 668 LEU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 87 ILE Chi-restraints excluded: chain s residue 106 VAL Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 50 LYS Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 3.9990 chunk 366 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 407 optimal weight: 2.9990 chunk 338 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 459 ASN ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 539 GLN o 671 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 650 ASN ** p 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1094 GLN p1115 GLN p1133 HIS ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 76 ASN v 126 GLN v 131 ASN w 45 GLN w 50 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 36597 Z= 0.516 Angle : 0.619 10.434 49911 Z= 0.324 Chirality : 0.046 0.207 5557 Planarity : 0.005 0.067 6097 Dihedral : 16.121 176.318 5807 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.03 % Favored : 94.83 % Rotamer: Outliers : 4.66 % Allowed : 17.14 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.49 (0.13), residues: 4137 helix: 1.48 (0.14), residues: 1404 sheet: 0.11 (0.19), residues: 671 loop : -0.35 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP q 49 HIS 0.012 0.002 HIS r 43 PHE 0.023 0.002 PHE q 229 TYR 0.018 0.002 TYR o 413 ARG 0.008 0.001 ARG q 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 549 time to evaluate : 3.914 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: o 16 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7159 (mtt-85) REVERT: o 18 ILE cc_start: 0.7745 (mt) cc_final: 0.7513 (mm) REVERT: o 58 MET cc_start: 0.7968 (ttp) cc_final: 0.7747 (ttm) REVERT: o 67 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7062 (tpp-160) REVERT: o 102 LYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6432 (tppt) REVERT: o 105 LYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4977 (tttt) REVERT: o 117 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7905 (tt) REVERT: o 140 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5097 (ttp80) REVERT: o 149 LYS cc_start: 0.7715 (ptpp) cc_final: 0.7473 (ptpp) REVERT: o 192 ARG cc_start: 0.7051 (ptm160) cc_final: 0.6786 (ptt180) REVERT: o 193 ARG cc_start: 0.7773 (ttp80) cc_final: 0.6991 (ttt180) REVERT: o 229 SER cc_start: 0.6582 (t) cc_final: 0.5889 (p) REVERT: o 234 PHE cc_start: 0.7531 (t80) cc_final: 0.7026 (t80) REVERT: o 266 MET cc_start: 0.3975 (mtm) cc_final: 0.3071 (ttp) REVERT: o 321 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6159 (mp0) REVERT: o 329 MET cc_start: 0.5318 (mpp) cc_final: 0.5007 (mmm) REVERT: o 411 SER cc_start: 0.7958 (m) cc_final: 0.7657 (p) REVERT: o 423 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7410 (p0) REVERT: o 426 ARG cc_start: 0.6704 (mtm-85) cc_final: 0.6440 (mtm-85) REVERT: o 451 CYS cc_start: 0.6799 (m) cc_final: 0.6171 (p) REVERT: o 565 MET cc_start: 0.7979 (tpt) cc_final: 0.7718 (tpt) REVERT: o 612 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7244 (p0) REVERT: o 673 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: o 728 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7168 (t) REVERT: o 796 LYS cc_start: 0.7509 (mttt) cc_final: 0.7064 (mttm) REVERT: o 803 LYS cc_start: 0.7422 (tttp) cc_final: 0.6917 (tptp) REVERT: o 818 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7363 (mp0) REVERT: o 868 MET cc_start: 0.7251 (ptt) cc_final: 0.7035 (ptt) REVERT: o 872 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7621 (ttm) REVERT: o 937 ASP cc_start: 0.7368 (t0) cc_final: 0.6947 (m-30) REVERT: o 950 ASN cc_start: 0.6472 (m-40) cc_final: 0.6184 (t0) REVERT: o 960 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.4784 (ttm-80) REVERT: o 962 ASP cc_start: 0.6925 (m-30) cc_final: 0.6591 (m-30) REVERT: o 1063 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6757 (pt0) REVERT: o 1085 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6128 (tp30) REVERT: o 1133 LYS cc_start: 0.8303 (mttt) cc_final: 0.8086 (mtmm) REVERT: o 1135 LYS cc_start: 0.7374 (mttt) cc_final: 0.7026 (mttp) REVERT: o 1144 LEU cc_start: 0.7849 (tp) cc_final: 0.7588 (tm) REVERT: o 1167 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.7073 (ttm-80) REVERT: o 1215 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6770 (tm-30) REVERT: o 1255 LEU cc_start: 0.7709 (mt) cc_final: 0.6873 (mt) REVERT: o 1262 MET cc_start: 0.6963 (ttt) cc_final: 0.6759 (tpp) REVERT: o 1279 MET cc_start: 0.6336 (ttp) cc_final: 0.5962 (ttp) REVERT: o 1281 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6777 (t70) REVERT: o 1284 PHE cc_start: 0.7393 (t80) cc_final: 0.7097 (t80) REVERT: o 1302 GLU cc_start: 0.7381 (pt0) cc_final: 0.6654 (mp0) REVERT: o 1303 GLN cc_start: 0.7840 (mt0) cc_final: 0.7465 (mp10) REVERT: o 1306 LYS cc_start: 0.5789 (mttt) cc_final: 0.5209 (mmmt) REVERT: o 1337 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6054 (mm-30) REVERT: o 1344 MET cc_start: 0.6387 (tpp) cc_final: 0.6145 (tpt) REVERT: o 1351 ASP cc_start: 0.7788 (m-30) cc_final: 0.7496 (m-30) REVERT: o 1422 GLN cc_start: 0.6891 (mt0) cc_final: 0.6138 (mm110) REVERT: o 1452 LYS cc_start: 0.6917 (mttt) cc_final: 0.6562 (mmtt) REVERT: p 94 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.7457 (t) REVERT: p 144 HIS cc_start: 0.6711 (m90) cc_final: 0.6332 (m170) REVERT: p 160 TYR cc_start: 0.7345 (m-80) cc_final: 0.6968 (m-80) REVERT: p 200 MET cc_start: 0.7881 (ttm) cc_final: 0.7386 (ttm) REVERT: p 222 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5687 (mtp85) REVERT: p 239 MET cc_start: 0.6576 (ttm) cc_final: 0.6229 (ttp) REVERT: p 254 GLN cc_start: 0.6196 (mt0) cc_final: 0.5725 (mp10) REVERT: p 309 PHE cc_start: 0.8639 (t80) cc_final: 0.8371 (t80) REVERT: p 312 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7203 (tm-30) REVERT: p 358 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6486 (pm20) REVERT: p 388 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: p 516 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: p 546 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6725 (mp0) REVERT: p 547 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6724 (tt0) REVERT: p 578 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7176 (mptp) REVERT: p 593 GLN cc_start: 0.6300 (mm-40) cc_final: 0.6047 (mt0) REVERT: p 597 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7950 (mp) REVERT: p 609 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5598 (mp0) REVERT: p 684 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6050 (mm-30) REVERT: p 728 MET cc_start: 0.7354 (mtm) cc_final: 0.6953 (mtp) REVERT: p 796 MET cc_start: 0.9003 (mtm) cc_final: 0.8414 (mtm) REVERT: p 798 ARG cc_start: 0.6695 (ttt90) cc_final: 0.6423 (tpt90) REVERT: p 817 GLN cc_start: 0.6317 (tt0) cc_final: 0.5657 (pm20) REVERT: p 827 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: p 850 ASP cc_start: 0.8204 (t0) cc_final: 0.7656 (p0) REVERT: p 916 TYR cc_start: 0.6678 (m-10) cc_final: 0.6183 (m-80) REVERT: p 958 CYS cc_start: 0.7806 (m) cc_final: 0.7403 (p) REVERT: p 976 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8162 (mtp) REVERT: p 995 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6877 (pt0) REVERT: p 1072 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6103 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7864 (tt0) cc_final: 0.7538 (tt0) REVERT: p 1131 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7594 (mtt180) REVERT: p 1151 MET cc_start: 0.8013 (ptm) cc_final: 0.7648 (ptp) REVERT: p 1172 MET cc_start: 0.6836 (mmt) cc_final: 0.6195 (mmt) REVERT: q 17 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6651 (mt-10) REVERT: q 44 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6336 (tp) REVERT: q 78 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6952 (tt) REVERT: q 81 LYS cc_start: 0.7266 (mtpt) cc_final: 0.6760 (mtmt) REVERT: q 83 GLN cc_start: 0.7721 (mt0) cc_final: 0.7306 (mt0) REVERT: q 96 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6355 (mp0) REVERT: q 102 THR cc_start: 0.7361 (m) cc_final: 0.7054 (p) REVERT: q 106 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7580 (ttp80) REVERT: q 108 ASN cc_start: 0.7726 (m-40) cc_final: 0.7245 (p0) REVERT: q 109 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7128 (pm20) REVERT: q 118 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7615 (ttm170) REVERT: q 126 ARG cc_start: 0.7586 (mtt180) cc_final: 0.6800 (mmm-85) REVERT: q 207 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: q 242 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: q 254 LYS cc_start: 0.6151 (tttt) cc_final: 0.5654 (mptt) REVERT: s 3 ASP cc_start: 0.6665 (m-30) cc_final: 0.6394 (m-30) REVERT: s 38 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7138 (mm-30) REVERT: s 61 LEU cc_start: 0.8260 (tp) cc_final: 0.7865 (tm) REVERT: s 71 GLN cc_start: 0.7781 (mt0) cc_final: 0.7566 (mt0) REVERT: s 79 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6912 (mp0) REVERT: s 125 TYR cc_start: 0.7104 (m-80) cc_final: 0.6818 (m-80) REVERT: s 159 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7558 (tp) REVERT: s 197 SER cc_start: 0.8617 (t) cc_final: 0.8346 (t) REVERT: t 57 MET cc_start: 0.7044 (ttp) cc_final: 0.6784 (ttm) REVERT: t 80 MET cc_start: 0.6395 (mmt) cc_final: 0.6151 (mmt) REVERT: t 86 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7104 (mm-30) REVERT: v 51 ASP cc_start: 0.7464 (m-30) cc_final: 0.7147 (t0) REVERT: v 55 LYS cc_start: 0.7388 (mtmt) cc_final: 0.7047 (ttmt) REVERT: v 79 ASP cc_start: 0.5952 (t0) cc_final: 0.5562 (t0) REVERT: v 87 GLN cc_start: 0.7581 (mp10) cc_final: 0.7148 (mm-40) REVERT: v 95 LYS cc_start: 0.6677 (tttt) cc_final: 0.6274 (ttmt) REVERT: v 100 GLU cc_start: 0.7308 (tt0) cc_final: 0.6601 (tt0) REVERT: v 133 HIS cc_start: 0.7792 (p-80) cc_final: 0.6885 (m170) REVERT: v 136 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6927 (mt-10) REVERT: v 146 LYS cc_start: 0.6589 (tttt) cc_final: 0.5915 (tttm) REVERT: w 56 ASN cc_start: 0.6908 (t0) cc_final: 0.6644 (t0) REVERT: w 71 ASP cc_start: 0.7673 (m-30) cc_final: 0.7362 (m-30) REVERT: w 109 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7793 (ptm160) REVERT: x 19 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: x 26 GLN cc_start: 0.7971 (tt0) cc_final: 0.7705 (tm-30) REVERT: x 57 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7934 (mm-30) REVERT: y 23 LYS cc_start: 0.8004 (mttt) cc_final: 0.7367 (mmmt) REVERT: y 38 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.5857 (mp0) REVERT: y 47 LYS cc_start: 0.6397 (ttpp) cc_final: 0.6162 (tttm) REVERT: y 48 SER cc_start: 0.7676 (t) cc_final: 0.7279 (p) REVERT: y 70 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7256 (ttmm) REVERT: z 21 GLU cc_start: 0.7053 (tt0) cc_final: 0.6671 (tt0) REVERT: z 25 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6194 (mp0) REVERT: z 35 ARG cc_start: 0.8041 (mtp85) cc_final: 0.7684 (ttp80) outliers start: 172 outliers final: 92 residues processed: 650 average time/residue: 1.6109 time to fit residues: 1249.0651 Evaluate side-chains 650 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 528 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 140 ARG Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 404 GLU Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 427 ILE Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 673 GLN Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 743 ARG Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 828 LEU Chi-restraints excluded: chain o residue 847 LEU Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1170 THR Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1367 THR Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 220 GLU Chi-restraints excluded: chain p residue 222 ARG Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 423 ILE Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 547 GLU Chi-restraints excluded: chain p residue 578 LYS Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 761 THR Chi-restraints excluded: chain p residue 763 SER Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 827 GLU Chi-restraints excluded: chain p residue 828 VAL Chi-restraints excluded: chain p residue 861 SER Chi-restraints excluded: chain p residue 896 LEU Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 242 GLU Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 17 LYS Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 110 LYS Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 chunk 232 optimal weight: 0.0010 chunk 297 optimal weight: 0.5980 chunk 230 optimal weight: 0.7980 chunk 342 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 765 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 525 ASN p 650 ASN p 718 GLN ** p 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1094 GLN p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 76 ASN w 22 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36597 Z= 0.150 Angle : 0.441 9.703 49911 Z= 0.237 Chirality : 0.039 0.162 5557 Planarity : 0.003 0.044 6097 Dihedral : 15.909 176.401 5807 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 27.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.06 % Favored : 95.79 % Rotamer: Outliers : 3.06 % Allowed : 19.33 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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 (0.13), residues: 4137 helix: 1.97 (0.14), residues: 1406 sheet: 0.24 (0.20), residues: 656 loop : -0.23 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 679 HIS 0.011 0.001 HIS r 43 PHE 0.022 0.001 PHE y 13 TYR 0.013 0.001 TYR t 115 ARG 0.005 0.000 ARG p 770 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 548 time to evaluate : 3.881 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: o 16 ARG cc_start: 0.7487 (mmt90) cc_final: 0.7143 (mtt-85) REVERT: o 18 ILE cc_start: 0.7715 (mt) cc_final: 0.7486 (mm) REVERT: o 58 MET cc_start: 0.7806 (ttp) cc_final: 0.7589 (ttm) REVERT: o 67 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7099 (tpp-160) REVERT: o 102 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6296 (tppt) REVERT: o 105 LYS cc_start: 0.5202 (OUTLIER) cc_final: 0.4937 (mttp) REVERT: o 117 LEU cc_start: 0.8279 (mt) cc_final: 0.7871 (tt) REVERT: o 140 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.5188 (ttp80) REVERT: o 149 LYS cc_start: 0.7739 (ptpp) cc_final: 0.7446 (ptpp) REVERT: o 192 ARG cc_start: 0.7074 (ptm160) cc_final: 0.6670 (ptt180) REVERT: o 193 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7011 (ttt180) REVERT: o 223 GLU cc_start: 0.6888 (tt0) cc_final: 0.6559 (tt0) REVERT: o 234 PHE cc_start: 0.7565 (t80) cc_final: 0.7064 (t80) REVERT: o 266 MET cc_start: 0.4000 (mtm) cc_final: 0.3057 (ttp) REVERT: o 321 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6082 (mp0) REVERT: o 329 MET cc_start: 0.5321 (mpp) cc_final: 0.5053 (mmm) REVERT: o 411 SER cc_start: 0.7967 (m) cc_final: 0.7662 (p) REVERT: o 423 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7341 (p0) REVERT: o 426 ARG cc_start: 0.6721 (mtm-85) cc_final: 0.6443 (mtm-85) REVERT: o 451 CYS cc_start: 0.6728 (m) cc_final: 0.6040 (p) REVERT: o 532 ARG cc_start: 0.6696 (ptm-80) cc_final: 0.6145 (ptt90) REVERT: o 559 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6739 (mt-10) REVERT: o 561 MET cc_start: 0.7247 (mtt) cc_final: 0.6987 (mmm) REVERT: o 565 MET cc_start: 0.7849 (tpt) cc_final: 0.7311 (tpt) REVERT: o 612 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7214 (p0) REVERT: o 728 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7209 (t) REVERT: o 761 SER cc_start: 0.7483 (m) cc_final: 0.6984 (t) REVERT: o 762 GLU cc_start: 0.7622 (mp0) cc_final: 0.7239 (mm-30) REVERT: o 796 LYS cc_start: 0.7294 (mttt) cc_final: 0.6822 (mttm) REVERT: o 803 LYS cc_start: 0.7401 (tttp) cc_final: 0.6901 (tptp) REVERT: o 818 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7266 (mp0) REVERT: o 845 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6263 (tt0) REVERT: o 868 MET cc_start: 0.7271 (ptt) cc_final: 0.7042 (ptt) REVERT: o 937 ASP cc_start: 0.7276 (t0) cc_final: 0.6952 (m-30) REVERT: o 960 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.4899 (ttm-80) REVERT: o 962 ASP cc_start: 0.6963 (m-30) cc_final: 0.6599 (m-30) REVERT: o 1063 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6608 (pt0) REVERT: o 1085 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6138 (tp30) REVERT: o 1133 LYS cc_start: 0.8340 (mttt) cc_final: 0.8138 (mtmm) REVERT: o 1135 LYS cc_start: 0.7298 (mttt) cc_final: 0.6933 (mttp) REVERT: o 1144 LEU cc_start: 0.7759 (tp) cc_final: 0.7500 (tm) REVERT: o 1167 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.6838 (ttm-80) REVERT: o 1262 MET cc_start: 0.7234 (ttt) cc_final: 0.6798 (tpp) REVERT: o 1279 MET cc_start: 0.6462 (ttp) cc_final: 0.6082 (ttp) REVERT: o 1281 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6366 (t70) REVERT: o 1284 PHE cc_start: 0.7366 (t80) cc_final: 0.7041 (t80) REVERT: o 1302 GLU cc_start: 0.7365 (pt0) cc_final: 0.6586 (mp0) REVERT: o 1303 GLN cc_start: 0.7868 (mt0) cc_final: 0.7536 (mp10) REVERT: o 1306 LYS cc_start: 0.5830 (mttt) cc_final: 0.5226 (mmmt) REVERT: o 1337 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6173 (mm-30) REVERT: o 1344 MET cc_start: 0.6370 (tpp) cc_final: 0.6048 (tpt) REVERT: o 1351 ASP cc_start: 0.7817 (m-30) cc_final: 0.7543 (m-30) REVERT: o 1422 GLN cc_start: 0.6877 (mt0) cc_final: 0.6157 (mm110) REVERT: o 1452 LYS cc_start: 0.6847 (mttt) cc_final: 0.6511 (mmtt) REVERT: p 91 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7363 (mp) REVERT: p 144 HIS cc_start: 0.6733 (m90) cc_final: 0.6427 (m170) REVERT: p 160 TYR cc_start: 0.7309 (m-80) cc_final: 0.7001 (m-80) REVERT: p 200 MET cc_start: 0.8036 (ttm) cc_final: 0.7528 (ttm) REVERT: p 222 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5786 (mtp85) REVERT: p 239 MET cc_start: 0.6679 (ttm) cc_final: 0.6246 (ttp) REVERT: p 309 PHE cc_start: 0.8627 (t80) cc_final: 0.8232 (t80) REVERT: p 312 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7144 (tm-30) REVERT: p 358 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6500 (pm20) REVERT: p 442 ASP cc_start: 0.5621 (m-30) cc_final: 0.5354 (m-30) REVERT: p 516 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: p 546 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6863 (mt-10) REVERT: p 547 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: p 563 ASP cc_start: 0.4301 (OUTLIER) cc_final: 0.2639 (m-30) REVERT: p 578 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7697 (mptt) REVERT: p 597 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7996 (mp) REVERT: p 684 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6252 (mm-30) REVERT: p 728 MET cc_start: 0.7047 (mtm) cc_final: 0.6627 (mtp) REVERT: p 768 ARG cc_start: 0.7664 (mpt90) cc_final: 0.7046 (mmm-85) REVERT: p 786 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7868 (p) REVERT: p 796 MET cc_start: 0.8980 (mtm) cc_final: 0.8504 (mtm) REVERT: p 798 ARG cc_start: 0.6611 (ttt90) cc_final: 0.6332 (tpt90) REVERT: p 817 GLN cc_start: 0.6420 (tt0) cc_final: 0.5742 (pm20) REVERT: p 827 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7602 (mt-10) REVERT: p 850 ASP cc_start: 0.8129 (t0) cc_final: 0.7695 (p0) REVERT: p 916 TYR cc_start: 0.6572 (m-10) cc_final: 0.6120 (m-80) REVERT: p 952 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: p 958 CYS cc_start: 0.7666 (m) cc_final: 0.7445 (p) REVERT: p 995 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7175 (mm-30) REVERT: p 1057 ASP cc_start: 0.7021 (m-30) cc_final: 0.6757 (m-30) REVERT: p 1076 GLU cc_start: 0.7764 (tt0) cc_final: 0.7431 (tm-30) REVERT: p 1131 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7766 (mtt180) REVERT: p 1151 MET cc_start: 0.7875 (ptm) cc_final: 0.7499 (ptp) REVERT: p 1172 MET cc_start: 0.6879 (mmt) cc_final: 0.6268 (mmt) REVERT: q 17 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6723 (mt-10) REVERT: q 78 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6730 (tt) REVERT: q 81 LYS cc_start: 0.7212 (mtpt) cc_final: 0.6818 (mtmt) REVERT: q 83 GLN cc_start: 0.7653 (mt0) cc_final: 0.7374 (mt0) REVERT: q 96 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6502 (mp0) REVERT: q 100 GLU cc_start: 0.7762 (tt0) cc_final: 0.7338 (tt0) REVERT: q 102 THR cc_start: 0.7389 (m) cc_final: 0.7052 (p) REVERT: q 106 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7575 (ttp80) REVERT: q 108 ASN cc_start: 0.7757 (m-40) cc_final: 0.7249 (p0) REVERT: q 109 GLU cc_start: 0.7568 (mt-10) cc_final: 0.6896 (pm20) REVERT: q 118 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7280 (ttm170) REVERT: q 126 ARG cc_start: 0.7553 (mtt180) cc_final: 0.6813 (mmm-85) REVERT: q 158 GLU cc_start: 0.7296 (tt0) cc_final: 0.6766 (tt0) REVERT: q 207 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: q 215 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6028 (mt-10) REVERT: q 254 LYS cc_start: 0.5950 (tttt) cc_final: 0.5505 (mptt) REVERT: s 3 ASP cc_start: 0.6596 (m-30) cc_final: 0.6337 (m-30) REVERT: s 38 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7185 (mm-30) REVERT: s 61 LEU cc_start: 0.8133 (tp) cc_final: 0.7705 (tm) REVERT: s 71 GLN cc_start: 0.7740 (mt0) cc_final: 0.7458 (mt0) REVERT: s 79 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6989 (mp0) REVERT: s 125 TYR cc_start: 0.6993 (m-80) cc_final: 0.6673 (m-80) REVERT: s 159 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7567 (tp) REVERT: s 197 SER cc_start: 0.8348 (t) cc_final: 0.7875 (t) REVERT: t 57 MET cc_start: 0.7106 (ttp) cc_final: 0.6771 (ttm) REVERT: t 80 MET cc_start: 0.6279 (mmt) cc_final: 0.5975 (mmt) REVERT: t 86 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7135 (mm-30) REVERT: v 36 LYS cc_start: 0.6452 (mmtt) cc_final: 0.6125 (mmpt) REVERT: v 51 ASP cc_start: 0.7216 (m-30) cc_final: 0.6786 (t0) REVERT: v 63 THR cc_start: 0.8887 (p) cc_final: 0.8660 (t) REVERT: v 71 ASP cc_start: 0.6524 (m-30) cc_final: 0.6101 (m-30) REVERT: v 79 ASP cc_start: 0.5757 (t0) cc_final: 0.5365 (t0) REVERT: v 87 GLN cc_start: 0.7631 (mp10) cc_final: 0.7202 (mm-40) REVERT: v 95 LYS cc_start: 0.6491 (tttt) cc_final: 0.6128 (ttmt) REVERT: v 100 GLU cc_start: 0.7107 (tt0) cc_final: 0.6318 (tt0) REVERT: v 132 LEU cc_start: 0.7154 (mt) cc_final: 0.6782 (mt) REVERT: v 133 HIS cc_start: 0.7731 (p-80) cc_final: 0.6875 (m170) REVERT: v 136 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6706 (mt-10) REVERT: v 146 LYS cc_start: 0.6610 (tttt) cc_final: 0.5947 (tttm) REVERT: w 56 ASN cc_start: 0.6796 (t0) cc_final: 0.6544 (t0) REVERT: w 71 ASP cc_start: 0.7760 (m-30) cc_final: 0.7464 (m-30) REVERT: x 13 ILE cc_start: 0.8761 (mm) cc_final: 0.8452 (mp) REVERT: x 19 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: x 26 GLN cc_start: 0.7911 (tt0) cc_final: 0.7651 (tm-30) REVERT: y 23 LYS cc_start: 0.7977 (mttt) cc_final: 0.7353 (mmmt) REVERT: y 38 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.5825 (mp0) REVERT: y 47 LYS cc_start: 0.6262 (ttpp) cc_final: 0.6011 (tttm) REVERT: y 48 SER cc_start: 0.7604 (t) cc_final: 0.7242 (p) REVERT: y 70 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7318 (ttmm) REVERT: z 15 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5429 (ttt) REVERT: z 25 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6157 (mp0) REVERT: z 35 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7579 (ttp80) outliers start: 113 outliers final: 55 residues processed: 618 average time/residue: 1.6280 time to fit residues: 1201.1131 Evaluate side-chains 600 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 521 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 140 ARG Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 427 ILE Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 828 LEU Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 220 GLU Chi-restraints excluded: chain p residue 222 ARG Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 423 ILE Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 547 GLU Chi-restraints excluded: chain p residue 563 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 644 LYS Chi-restraints excluded: chain p residue 674 MET Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 257 optimal weight: 2.9990 chunk 276 optimal weight: 0.0670 chunk 200 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 318 optimal weight: 50.0000 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 485 ASN o 673 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 650 ASN ** p 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 76 ASN w 22 ASN w 87 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36597 Z= 0.247 Angle : 0.469 9.954 49911 Z= 0.250 Chirality : 0.040 0.162 5557 Planarity : 0.003 0.044 6097 Dihedral : 15.854 175.961 5807 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 3.61 % Allowed : 19.17 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.85 (0.13), residues: 4137 helix: 1.96 (0.14), residues: 1407 sheet: 0.25 (0.20), residues: 654 loop : -0.26 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 679 HIS 0.017 0.001 HIS r 43 PHE 0.027 0.001 PHE y 13 TYR 0.016 0.001 TYR t 115 ARG 0.004 0.000 ARG z 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 525 time to evaluate : 4.016 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: o 16 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7115 (mtt-85) REVERT: o 18 ILE cc_start: 0.7738 (mt) cc_final: 0.7503 (mm) REVERT: o 58 MET cc_start: 0.7821 (ttp) cc_final: 0.7610 (ttm) REVERT: o 67 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7183 (tpp-160) REVERT: o 105 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4952 (mttp) REVERT: o 140 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5301 (ttp80) REVERT: o 149 LYS cc_start: 0.7701 (ptpp) cc_final: 0.7461 (ptpp) REVERT: o 193 ARG cc_start: 0.7696 (ttp80) cc_final: 0.6849 (ttt180) REVERT: o 223 GLU cc_start: 0.6825 (tt0) cc_final: 0.6492 (tt0) REVERT: o 234 PHE cc_start: 0.7608 (t80) cc_final: 0.7119 (t80) REVERT: o 266 MET cc_start: 0.4117 (mtm) cc_final: 0.3173 (ttp) REVERT: o 321 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6065 (mp0) REVERT: o 329 MET cc_start: 0.5374 (mpp) cc_final: 0.5103 (mmm) REVERT: o 411 SER cc_start: 0.7973 (m) cc_final: 0.7682 (p) REVERT: o 423 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7360 (p0) REVERT: o 451 CYS cc_start: 0.6714 (m) cc_final: 0.6021 (p) REVERT: o 561 MET cc_start: 0.7316 (mtt) cc_final: 0.7070 (mmm) REVERT: o 612 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7217 (p0) REVERT: o 683 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.5614 (tp30) REVERT: o 728 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7170 (t) REVERT: o 761 SER cc_start: 0.7471 (m) cc_final: 0.6961 (t) REVERT: o 762 GLU cc_start: 0.7609 (mp0) cc_final: 0.7238 (mm-30) REVERT: o 796 LYS cc_start: 0.7373 (mttt) cc_final: 0.6934 (mttm) REVERT: o 803 LYS cc_start: 0.7426 (tttp) cc_final: 0.6937 (tptp) REVERT: o 818 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7275 (mp0) REVERT: o 845 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6317 (tt0) REVERT: o 868 MET cc_start: 0.7267 (ptt) cc_final: 0.7039 (ptt) REVERT: o 937 ASP cc_start: 0.7284 (t0) cc_final: 0.6953 (m-30) REVERT: o 960 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.4826 (ttm-80) REVERT: o 962 ASP cc_start: 0.6965 (m-30) cc_final: 0.6614 (m-30) REVERT: o 1063 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6698 (pt0) REVERT: o 1085 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6131 (tp30) REVERT: o 1133 LYS cc_start: 0.8336 (mttt) cc_final: 0.8116 (mtmm) REVERT: o 1135 LYS cc_start: 0.7378 (mttt) cc_final: 0.6951 (mttp) REVERT: o 1144 LEU cc_start: 0.7788 (tp) cc_final: 0.7519 (tm) REVERT: o 1167 ARG cc_start: 0.7441 (ttp-110) cc_final: 0.6881 (ttm-80) REVERT: o 1262 MET cc_start: 0.7228 (ttt) cc_final: 0.6793 (tpp) REVERT: o 1279 MET cc_start: 0.6482 (ttp) cc_final: 0.6091 (ttp) REVERT: o 1281 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.6725 (t70) REVERT: o 1284 PHE cc_start: 0.7445 (t80) cc_final: 0.7145 (t80) REVERT: o 1302 GLU cc_start: 0.7354 (pt0) cc_final: 0.6620 (mp0) REVERT: o 1303 GLN cc_start: 0.7871 (mt0) cc_final: 0.7520 (mp10) REVERT: o 1306 LYS cc_start: 0.5797 (mttt) cc_final: 0.5200 (mmmt) REVERT: o 1337 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6161 (mm-30) REVERT: o 1344 MET cc_start: 0.6393 (tpp) cc_final: 0.6071 (tpt) REVERT: o 1351 ASP cc_start: 0.7794 (m-30) cc_final: 0.7525 (m-30) REVERT: o 1422 GLN cc_start: 0.6880 (mt0) cc_final: 0.6175 (mm110) REVERT: o 1452 LYS cc_start: 0.6844 (mttt) cc_final: 0.6502 (mmtt) REVERT: p 144 HIS cc_start: 0.6761 (m90) cc_final: 0.6423 (m170) REVERT: p 200 MET cc_start: 0.8024 (ttm) cc_final: 0.7522 (ttm) REVERT: p 222 ARG cc_start: 0.6351 (OUTLIER) cc_final: 0.5806 (mtp85) REVERT: p 239 MET cc_start: 0.6589 (ttm) cc_final: 0.6188 (ttp) REVERT: p 254 GLN cc_start: 0.6147 (mt0) cc_final: 0.5708 (mp10) REVERT: p 309 PHE cc_start: 0.8630 (t80) cc_final: 0.8240 (t80) REVERT: p 312 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7006 (tm-30) REVERT: p 358 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6482 (pm20) REVERT: p 388 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: p 483 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.5894 (mtp-110) REVERT: p 516 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: p 546 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6704 (mp0) REVERT: p 547 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: p 563 ASP cc_start: 0.4370 (OUTLIER) cc_final: 0.3876 (m-30) REVERT: p 578 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7631 (mptm) REVERT: p 597 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7933 (mp) REVERT: p 650 ASN cc_start: 0.7798 (m-40) cc_final: 0.7538 (m-40) REVERT: p 684 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6247 (mm-30) REVERT: p 728 MET cc_start: 0.7153 (mtm) cc_final: 0.6675 (mtp) REVERT: p 786 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7839 (p) REVERT: p 796 MET cc_start: 0.9001 (mtm) cc_final: 0.8540 (mtm) REVERT: p 798 ARG cc_start: 0.6702 (ttt90) cc_final: 0.6428 (tpt90) REVERT: p 817 GLN cc_start: 0.6267 (tt0) cc_final: 0.5746 (pm20) REVERT: p 850 ASP cc_start: 0.8179 (t0) cc_final: 0.7675 (p0) REVERT: p 916 TYR cc_start: 0.6595 (m-10) cc_final: 0.6113 (m-80) REVERT: p 952 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: p 958 CYS cc_start: 0.7764 (m) cc_final: 0.7464 (p) REVERT: p 995 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7168 (mm-30) REVERT: p 1057 ASP cc_start: 0.7027 (m-30) cc_final: 0.6804 (m-30) REVERT: p 1072 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.5645 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7738 (tt0) cc_final: 0.7400 (tm-30) REVERT: p 1131 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7720 (mtt180) REVERT: p 1151 MET cc_start: 0.7924 (ptm) cc_final: 0.7543 (ptp) REVERT: p 1172 MET cc_start: 0.6858 (mmt) cc_final: 0.6243 (mmt) REVERT: q 17 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6719 (mt-10) REVERT: q 78 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6812 (tt) REVERT: q 81 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6840 (mtmt) REVERT: q 83 GLN cc_start: 0.7660 (mt0) cc_final: 0.7420 (mt0) REVERT: q 96 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6512 (mp0) REVERT: q 102 THR cc_start: 0.7456 (m) cc_final: 0.7115 (p) REVERT: q 106 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7573 (ttp80) REVERT: q 108 ASN cc_start: 0.7881 (m-40) cc_final: 0.7281 (p0) REVERT: q 109 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7017 (pm20) REVERT: q 118 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7565 (ttm170) REVERT: q 126 ARG cc_start: 0.7560 (mtt180) cc_final: 0.6813 (mmm-85) REVERT: q 207 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: q 215 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6012 (mt-10) REVERT: q 254 LYS cc_start: 0.5999 (tttt) cc_final: 0.5536 (mptt) REVERT: s 3 ASP cc_start: 0.6614 (m-30) cc_final: 0.6354 (m-30) REVERT: s 38 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7184 (mm-30) REVERT: s 61 LEU cc_start: 0.8131 (tp) cc_final: 0.7707 (tm) REVERT: s 79 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6992 (mp0) REVERT: s 125 TYR cc_start: 0.6966 (m-80) cc_final: 0.6634 (m-80) REVERT: s 159 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7600 (tp) REVERT: s 197 SER cc_start: 0.8322 (t) cc_final: 0.7855 (t) REVERT: t 57 MET cc_start: 0.7116 (ttp) cc_final: 0.6780 (ttm) REVERT: t 80 MET cc_start: 0.6273 (mmt) cc_final: 0.5971 (mmt) REVERT: t 86 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7048 (mm-30) REVERT: v 51 ASP cc_start: 0.7208 (m-30) cc_final: 0.6747 (t0) REVERT: v 55 LYS cc_start: 0.7399 (mtmt) cc_final: 0.6924 (ttmm) REVERT: v 79 ASP cc_start: 0.5906 (t0) cc_final: 0.5565 (t0) REVERT: v 87 GLN cc_start: 0.7643 (mp10) cc_final: 0.7214 (mm-40) REVERT: v 95 LYS cc_start: 0.6462 (tttt) cc_final: 0.6191 (ttmt) REVERT: v 100 GLU cc_start: 0.7285 (tt0) cc_final: 0.6537 (tt0) REVERT: v 132 LEU cc_start: 0.7235 (mt) cc_final: 0.6892 (mt) REVERT: v 133 HIS cc_start: 0.7751 (p-80) cc_final: 0.6826 (m170) REVERT: v 136 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6917 (mt-10) REVERT: v 146 LYS cc_start: 0.6555 (tttt) cc_final: 0.5834 (tttm) REVERT: w 56 ASN cc_start: 0.6778 (t0) cc_final: 0.6543 (t0) REVERT: w 71 ASP cc_start: 0.7804 (m-30) cc_final: 0.7501 (m-30) REVERT: x 13 ILE cc_start: 0.8751 (mm) cc_final: 0.8471 (mp) REVERT: x 19 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: x 26 GLN cc_start: 0.7957 (tt0) cc_final: 0.7723 (tm-30) REVERT: y 23 LYS cc_start: 0.7976 (mttt) cc_final: 0.7354 (mmmt) REVERT: y 38 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.5819 (mp0) REVERT: y 47 LYS cc_start: 0.6283 (ttpp) cc_final: 0.6031 (tttm) REVERT: y 48 SER cc_start: 0.7603 (t) cc_final: 0.7233 (p) REVERT: y 70 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7234 (ttmm) REVERT: z 25 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6165 (mp0) REVERT: z 35 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7587 (ttp80) outliers start: 133 outliers final: 79 residues processed: 604 average time/residue: 1.6656 time to fit residues: 1206.2482 Evaluate side-chains 616 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 511 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 140 ARG Chi-restraints excluded: chain o residue 196 LEU Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 404 GLU Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 427 ILE Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 828 LEU Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 220 GLU Chi-restraints excluded: chain p residue 222 ARG Chi-restraints excluded: chain p residue 288 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 423 ILE Chi-restraints excluded: chain p residue 483 ARG Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 547 GLU Chi-restraints excluded: chain p residue 563 ASP Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 578 LYS Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 644 LYS Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 840 MET Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 110 LEU Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 68 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 50 LYS Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 50.0000 chunk 388 optimal weight: 3.9990 chunk 354 optimal weight: 0.1980 chunk 378 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 341 optimal weight: 2.9990 chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 204 HIS ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 GLN ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 582 GLN ** p 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5366 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36597 Z= 0.318 Angle : 0.506 10.004 49911 Z= 0.269 Chirality : 0.042 0.176 5557 Planarity : 0.004 0.046 6097 Dihedral : 15.834 174.947 5807 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 27.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.54 % Rotamer: Outliers : 3.61 % Allowed : 19.17 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.66 (0.13), residues: 4137 helix: 1.76 (0.14), residues: 1405 sheet: 0.19 (0.20), residues: 654 loop : -0.37 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 49 HIS 0.020 0.001 HIS r 43 PHE 0.022 0.002 PHE y 13 TYR 0.016 0.002 TYR t 115 ARG 0.004 0.000 ARG p 592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 519 time to evaluate : 3.830 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: o 16 ARG cc_start: 0.7390 (mmt90) cc_final: 0.7134 (mtt-85) REVERT: o 18 ILE cc_start: 0.7764 (mt) cc_final: 0.7533 (mm) REVERT: o 58 MET cc_start: 0.7831 (ttp) cc_final: 0.7620 (ttm) REVERT: o 67 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7203 (tpp-160) REVERT: o 102 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6355 (tppt) REVERT: o 105 LYS cc_start: 0.5482 (OUTLIER) cc_final: 0.5217 (mttp) REVERT: o 140 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.5154 (ttp80) REVERT: o 192 ARG cc_start: 0.7226 (ptt90) cc_final: 0.6914 (ptt180) REVERT: o 193 ARG cc_start: 0.7540 (ttp80) cc_final: 0.6900 (ttp-170) REVERT: o 223 GLU cc_start: 0.6801 (tt0) cc_final: 0.6465 (tt0) REVERT: o 234 PHE cc_start: 0.7650 (t80) cc_final: 0.7143 (t80) REVERT: o 266 MET cc_start: 0.4196 (mtm) cc_final: 0.3286 (ttp) REVERT: o 321 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6046 (mp0) REVERT: o 411 SER cc_start: 0.7958 (m) cc_final: 0.7666 (p) REVERT: o 423 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7423 (p0) REVERT: o 451 CYS cc_start: 0.6827 (m) cc_final: 0.6090 (p) REVERT: o 561 MET cc_start: 0.7353 (mtt) cc_final: 0.7113 (mmm) REVERT: o 612 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7225 (p0) REVERT: o 728 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7291 (t) REVERT: o 761 SER cc_start: 0.7459 (m) cc_final: 0.6871 (t) REVERT: o 762 GLU cc_start: 0.7727 (mp0) cc_final: 0.7277 (mm-30) REVERT: o 796 LYS cc_start: 0.7444 (mttt) cc_final: 0.6982 (mttm) REVERT: o 803 LYS cc_start: 0.7372 (tttp) cc_final: 0.6915 (tptp) REVERT: o 818 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7373 (mp0) REVERT: o 845 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6462 (tt0) REVERT: o 868 MET cc_start: 0.7252 (ptt) cc_final: 0.7023 (ptt) REVERT: o 937 ASP cc_start: 0.7187 (t0) cc_final: 0.6849 (m-30) REVERT: o 960 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.4807 (ttm-80) REVERT: o 962 ASP cc_start: 0.6932 (m-30) cc_final: 0.6590 (m-30) REVERT: o 1063 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6631 (pt0) REVERT: o 1085 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6157 (tp30) REVERT: o 1133 LYS cc_start: 0.8298 (mttt) cc_final: 0.8087 (mtmm) REVERT: o 1135 LYS cc_start: 0.7424 (mttt) cc_final: 0.7036 (mttp) REVERT: o 1144 LEU cc_start: 0.7777 (tp) cc_final: 0.7524 (tm) REVERT: o 1167 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.6966 (ttm-80) REVERT: o 1262 MET cc_start: 0.6946 (ttt) cc_final: 0.6685 (tpp) REVERT: o 1279 MET cc_start: 0.6463 (ttp) cc_final: 0.6049 (ttp) REVERT: o 1281 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.6652 (t70) REVERT: o 1284 PHE cc_start: 0.7473 (t80) cc_final: 0.7179 (t80) REVERT: o 1302 GLU cc_start: 0.7367 (pt0) cc_final: 0.6568 (mp0) REVERT: o 1303 GLN cc_start: 0.7857 (mt0) cc_final: 0.7489 (mp10) REVERT: o 1306 LYS cc_start: 0.5721 (mttt) cc_final: 0.5139 (mmmt) REVERT: o 1337 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5735 (mt-10) REVERT: o 1344 MET cc_start: 0.6372 (tpp) cc_final: 0.6050 (tpt) REVERT: o 1351 ASP cc_start: 0.7786 (m-30) cc_final: 0.7524 (m-30) REVERT: o 1422 GLN cc_start: 0.6844 (mt0) cc_final: 0.6147 (mm110) REVERT: o 1452 LYS cc_start: 0.6815 (mttt) cc_final: 0.6477 (mmtt) REVERT: p 94 SER cc_start: 0.7620 (OUTLIER) cc_final: 0.7407 (t) REVERT: p 144 HIS cc_start: 0.6716 (m90) cc_final: 0.6378 (m170) REVERT: p 200 MET cc_start: 0.7989 (ttm) cc_final: 0.7396 (ttm) REVERT: p 222 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.5747 (mtp85) REVERT: p 239 MET cc_start: 0.6572 (ttm) cc_final: 0.6117 (ttp) REVERT: p 254 GLN cc_start: 0.6195 (mt0) cc_final: 0.5605 (mp10) REVERT: p 309 PHE cc_start: 0.8635 (t80) cc_final: 0.8279 (t80) REVERT: p 312 GLN cc_start: 0.7396 (tm-30) cc_final: 0.6911 (tm-30) REVERT: p 358 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6196 (pm20) REVERT: p 388 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: p 483 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6224 (mtp-110) REVERT: p 546 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6725 (mp0) REVERT: p 547 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6767 (tt0) REVERT: p 563 ASP cc_start: 0.4879 (OUTLIER) cc_final: 0.2935 (m-30) REVERT: p 578 LYS cc_start: 0.8039 (mmtp) cc_final: 0.7704 (mptt) REVERT: p 582 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: p 597 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7960 (mp) REVERT: p 609 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5476 (mp0) REVERT: p 650 ASN cc_start: 0.7805 (m-40) cc_final: 0.7557 (m-40) REVERT: p 684 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6152 (mm-30) REVERT: p 728 MET cc_start: 0.7219 (mtm) cc_final: 0.6779 (mtp) REVERT: p 786 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7771 (p) REVERT: p 796 MET cc_start: 0.9054 (mtm) cc_final: 0.8532 (mtm) REVERT: p 798 ARG cc_start: 0.6688 (ttt90) cc_final: 0.6414 (tpt90) REVERT: p 817 GLN cc_start: 0.6323 (tt0) cc_final: 0.5674 (pm20) REVERT: p 850 ASP cc_start: 0.8196 (t0) cc_final: 0.7684 (p0) REVERT: p 916 TYR cc_start: 0.6689 (m-10) cc_final: 0.6151 (m-80) REVERT: p 958 CYS cc_start: 0.7811 (m) cc_final: 0.7464 (p) REVERT: p 995 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7178 (mm-30) REVERT: p 1057 ASP cc_start: 0.6970 (m-30) cc_final: 0.6770 (m-30) REVERT: p 1072 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.5947 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7734 (tt0) cc_final: 0.7412 (tm-30) REVERT: p 1151 MET cc_start: 0.7966 (ptm) cc_final: 0.7456 (ptm) REVERT: p 1172 MET cc_start: 0.6764 (mmt) cc_final: 0.6139 (mmt) REVERT: q 17 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6634 (mt-10) REVERT: q 78 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6930 (tt) REVERT: q 81 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6456 (mttt) REVERT: q 83 GLN cc_start: 0.7665 (mt0) cc_final: 0.7407 (mt0) REVERT: q 96 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6488 (mp0) REVERT: q 102 THR cc_start: 0.7408 (m) cc_final: 0.7085 (p) REVERT: q 106 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7457 (ttm-80) REVERT: q 108 ASN cc_start: 0.7922 (m-40) cc_final: 0.7561 (m-40) REVERT: q 109 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7082 (pm20) REVERT: q 111 GLN cc_start: 0.7843 (tt0) cc_final: 0.7264 (mp10) REVERT: q 118 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: q 126 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6898 (mmm-85) REVERT: q 158 GLU cc_start: 0.7286 (tt0) cc_final: 0.6855 (tt0) REVERT: q 207 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7250 (pt0) REVERT: q 215 GLU cc_start: 0.6465 (mt-10) cc_final: 0.6046 (mt-10) REVERT: q 254 LYS cc_start: 0.6140 (tttt) cc_final: 0.5702 (mptt) REVERT: r 39 MET cc_start: 0.8688 (ptt) cc_final: 0.8475 (ppp) REVERT: s 38 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7220 (mm-30) REVERT: s 61 LEU cc_start: 0.8150 (tp) cc_final: 0.7697 (tm) REVERT: s 79 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7017 (mp0) REVERT: s 121 MET cc_start: 0.7407 (ptp) cc_final: 0.7061 (pmm) REVERT: s 125 TYR cc_start: 0.6998 (m-80) cc_final: 0.6648 (m-80) REVERT: s 159 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7561 (tp) REVERT: s 197 SER cc_start: 0.8327 (t) cc_final: 0.7877 (t) REVERT: t 57 MET cc_start: 0.7148 (ttp) cc_final: 0.6827 (ttm) REVERT: t 80 MET cc_start: 0.6226 (mmt) cc_final: 0.6022 (mmt) REVERT: t 86 GLU cc_start: 0.7765 (mm-30) cc_final: 0.6878 (mm-30) REVERT: v 51 ASP cc_start: 0.7159 (m-30) cc_final: 0.6712 (t0) REVERT: v 55 LYS cc_start: 0.7381 (mtmt) cc_final: 0.6845 (ttmm) REVERT: v 79 ASP cc_start: 0.6027 (t0) cc_final: 0.5730 (t0) REVERT: v 87 GLN cc_start: 0.7676 (mp10) cc_final: 0.7211 (mm-40) REVERT: v 95 LYS cc_start: 0.6480 (tttt) cc_final: 0.6181 (ttmt) REVERT: v 100 GLU cc_start: 0.7331 (tt0) cc_final: 0.6508 (tt0) REVERT: v 132 LEU cc_start: 0.7249 (mt) cc_final: 0.6909 (mt) REVERT: v 133 HIS cc_start: 0.7895 (p-80) cc_final: 0.6988 (m170) REVERT: v 136 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6889 (mt-10) REVERT: v 146 LYS cc_start: 0.6552 (tttt) cc_final: 0.5824 (tttm) REVERT: w 56 ASN cc_start: 0.6504 (t0) cc_final: 0.6282 (t0) REVERT: w 71 ASP cc_start: 0.7676 (m-30) cc_final: 0.7374 (m-30) REVERT: x 13 ILE cc_start: 0.8724 (mm) cc_final: 0.8445 (mp) REVERT: x 19 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: x 26 GLN cc_start: 0.7952 (tt0) cc_final: 0.7711 (tm-30) REVERT: y 23 LYS cc_start: 0.7933 (mttt) cc_final: 0.7352 (mmmt) REVERT: y 38 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: y 47 LYS cc_start: 0.6325 (ttpp) cc_final: 0.6083 (tttm) REVERT: y 48 SER cc_start: 0.7625 (t) cc_final: 0.7244 (p) REVERT: y 70 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7184 (ttmm) REVERT: z 25 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6176 (mp0) REVERT: z 35 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7581 (ttp80) REVERT: z 39 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6362 (p) outliers start: 133 outliers final: 82 residues processed: 601 average time/residue: 1.6244 time to fit residues: 1157.9409 Evaluate side-chains 618 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 509 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 140 ARG Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 336 LEU Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 404 GLU Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 427 ILE Chi-restraints excluded: chain o residue 485 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 828 LEU Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1207 ILE Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 220 GLU Chi-restraints excluded: chain p residue 222 ARG Chi-restraints excluded: chain p residue 288 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 483 ARG Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 547 GLU Chi-restraints excluded: chain p residue 563 ASP Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 644 LYS Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 759 VAL Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 840 MET Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain s residue 120 ASP Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 110 LEU Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 110 THR Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain z residue 15 MET Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 39 CYS Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.0470 chunk 399 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 chunk 419 optimal weight: 0.7980 chunk 386 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 582 GLN ** p 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36597 Z= 0.200 Angle : 0.461 9.858 49911 Z= 0.246 Chirality : 0.040 0.160 5557 Planarity : 0.003 0.042 6097 Dihedral : 15.771 174.781 5807 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.85 % Rotamer: Outliers : 3.06 % Allowed : 19.85 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.76 (0.13), residues: 4137 helix: 1.90 (0.14), residues: 1407 sheet: 0.21 (0.20), residues: 654 loop : -0.33 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 679 HIS 0.017 0.001 HIS r 43 PHE 0.018 0.001 PHE y 13 TYR 0.016 0.001 TYR t 115 ARG 0.004 0.000 ARG v 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 529 time to evaluate : 3.984 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: o 16 ARG cc_start: 0.7387 (mmt90) cc_final: 0.7128 (mtt-85) REVERT: o 18 ILE cc_start: 0.7743 (mt) cc_final: 0.7521 (mm) REVERT: o 37 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6736 (p) REVERT: o 58 MET cc_start: 0.7810 (ttp) cc_final: 0.7597 (ttm) REVERT: o 67 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7195 (tpp-160) REVERT: o 70 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6494 (mmm160) REVERT: o 102 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.6220 (tppt) REVERT: o 105 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5315 (mttp) REVERT: o 140 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5292 (ttp80) REVERT: o 192 ARG cc_start: 0.7354 (ptt90) cc_final: 0.7067 (ptt180) REVERT: o 193 ARG cc_start: 0.7548 (ttp80) cc_final: 0.6933 (ttp-170) REVERT: o 223 GLU cc_start: 0.6808 (tt0) cc_final: 0.6468 (tt0) REVERT: o 234 PHE cc_start: 0.7658 (t80) cc_final: 0.7168 (t80) REVERT: o 266 MET cc_start: 0.4203 (mtm) cc_final: 0.3292 (ttp) REVERT: o 321 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6023 (mp0) REVERT: o 329 MET cc_start: 0.5296 (mpp) cc_final: 0.4947 (mmm) REVERT: o 411 SER cc_start: 0.7957 (m) cc_final: 0.7664 (p) REVERT: o 423 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7424 (p0) REVERT: o 451 CYS cc_start: 0.6832 (m) cc_final: 0.6076 (p) REVERT: o 561 MET cc_start: 0.7304 (mtt) cc_final: 0.7059 (mmm) REVERT: o 612 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7235 (p0) REVERT: o 728 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7274 (t) REVERT: o 761 SER cc_start: 0.7582 (m) cc_final: 0.7041 (t) REVERT: o 762 GLU cc_start: 0.7625 (mp0) cc_final: 0.7247 (mm-30) REVERT: o 796 LYS cc_start: 0.7408 (mttt) cc_final: 0.6956 (mttm) REVERT: o 803 LYS cc_start: 0.7382 (tttp) cc_final: 0.6893 (tptp) REVERT: o 818 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7382 (mp0) REVERT: o 845 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: o 868 MET cc_start: 0.7253 (ptt) cc_final: 0.7041 (ptt) REVERT: o 937 ASP cc_start: 0.7170 (t0) cc_final: 0.6857 (m-30) REVERT: o 960 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4809 (ttm-80) REVERT: o 962 ASP cc_start: 0.6964 (m-30) cc_final: 0.6614 (m-30) REVERT: o 1063 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6605 (pt0) REVERT: o 1085 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6145 (tp30) REVERT: o 1133 LYS cc_start: 0.8303 (mttt) cc_final: 0.8093 (mtmm) REVERT: o 1135 LYS cc_start: 0.7647 (mttt) cc_final: 0.7257 (mttp) REVERT: o 1144 LEU cc_start: 0.7768 (tp) cc_final: 0.7514 (tm) REVERT: o 1167 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.6872 (ttm-80) REVERT: o 1279 MET cc_start: 0.6491 (ttp) cc_final: 0.6064 (ttp) REVERT: o 1281 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.6838 (t70) REVERT: o 1284 PHE cc_start: 0.7456 (t80) cc_final: 0.7177 (t80) REVERT: o 1302 GLU cc_start: 0.7353 (pt0) cc_final: 0.6612 (mp0) REVERT: o 1303 GLN cc_start: 0.7851 (mt0) cc_final: 0.7492 (mp10) REVERT: o 1306 LYS cc_start: 0.5780 (mttt) cc_final: 0.5191 (mmmt) REVERT: o 1337 GLU cc_start: 0.6326 (mt-10) cc_final: 0.5776 (mt-10) REVERT: o 1344 MET cc_start: 0.6377 (tpp) cc_final: 0.6061 (tpt) REVERT: o 1351 ASP cc_start: 0.7792 (m-30) cc_final: 0.7533 (m-30) REVERT: o 1422 GLN cc_start: 0.6830 (mt0) cc_final: 0.6121 (mm110) REVERT: o 1452 LYS cc_start: 0.6803 (mttt) cc_final: 0.6465 (mmtt) REVERT: p 91 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7345 (mp) REVERT: p 144 HIS cc_start: 0.6734 (m90) cc_final: 0.6386 (m170) REVERT: p 200 MET cc_start: 0.7979 (ttm) cc_final: 0.7333 (ttm) REVERT: p 222 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5771 (mtt-85) REVERT: p 239 MET cc_start: 0.6567 (ttm) cc_final: 0.6107 (ttp) REVERT: p 254 GLN cc_start: 0.6179 (mt0) cc_final: 0.5588 (mp10) REVERT: p 309 PHE cc_start: 0.8624 (t80) cc_final: 0.8286 (t80) REVERT: p 312 GLN cc_start: 0.7339 (tm-30) cc_final: 0.6969 (tm-30) REVERT: p 358 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6395 (pm20) REVERT: p 388 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: p 483 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.5777 (mtp-110) REVERT: p 516 GLU cc_start: 0.7163 (mp0) cc_final: 0.6851 (mp0) REVERT: p 546 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6717 (mp0) REVERT: p 563 ASP cc_start: 0.4818 (OUTLIER) cc_final: 0.4064 (m-30) REVERT: p 578 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7740 (mptp) REVERT: p 582 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: p 597 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7953 (mp) REVERT: p 650 ASN cc_start: 0.7783 (m-40) cc_final: 0.7527 (m-40) REVERT: p 684 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6178 (mm-30) REVERT: p 728 MET cc_start: 0.7138 (mtm) cc_final: 0.6705 (mtp) REVERT: p 786 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7831 (p) REVERT: p 796 MET cc_start: 0.9002 (mtm) cc_final: 0.8446 (mtm) REVERT: p 798 ARG cc_start: 0.6681 (ttt90) cc_final: 0.6409 (tpt90) REVERT: p 817 GLN cc_start: 0.6292 (tt0) cc_final: 0.5668 (pm20) REVERT: p 850 ASP cc_start: 0.8196 (t0) cc_final: 0.7701 (p0) REVERT: p 916 TYR cc_start: 0.6684 (m-10) cc_final: 0.6135 (m-80) REVERT: p 942 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7827 (pttt) REVERT: p 952 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: p 958 CYS cc_start: 0.7791 (m) cc_final: 0.7467 (p) REVERT: p 995 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7148 (mm-30) REVERT: p 1057 ASP cc_start: 0.6875 (m-30) cc_final: 0.6672 (m-30) REVERT: p 1072 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.5687 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7747 (tt0) cc_final: 0.7404 (tm-30) REVERT: p 1131 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7603 (mtt180) REVERT: p 1151 MET cc_start: 0.7929 (ptm) cc_final: 0.7419 (ptm) REVERT: p 1172 MET cc_start: 0.6725 (mmt) cc_final: 0.6147 (mmt) REVERT: q 17 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6599 (pm20) REVERT: q 44 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6173 (tp) REVERT: q 78 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.6856 (tt) REVERT: q 81 LYS cc_start: 0.7252 (mtpt) cc_final: 0.6846 (mtmt) REVERT: q 83 GLN cc_start: 0.7656 (mt0) cc_final: 0.7403 (mt0) REVERT: q 96 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6488 (mp0) REVERT: q 102 THR cc_start: 0.7408 (m) cc_final: 0.7089 (p) REVERT: q 106 ARG cc_start: 0.8041 (ttt180) cc_final: 0.7523 (ttp80) REVERT: q 108 ASN cc_start: 0.7939 (m-40) cc_final: 0.7281 (p0) REVERT: q 109 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7032 (pm20) REVERT: q 111 GLN cc_start: 0.7851 (tt0) cc_final: 0.7231 (mp10) REVERT: q 118 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7555 (ttm170) REVERT: q 126 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6815 (mmm-85) REVERT: q 158 GLU cc_start: 0.7294 (tt0) cc_final: 0.6804 (tt0) REVERT: q 207 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: q 215 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6059 (mt-10) REVERT: q 254 LYS cc_start: 0.5987 (tttt) cc_final: 0.5517 (mptt) REVERT: r 39 MET cc_start: 0.8660 (ptt) cc_final: 0.8448 (ppp) REVERT: s 3 ASP cc_start: 0.6495 (m-30) cc_final: 0.6201 (m-30) REVERT: s 38 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7218 (mm-30) REVERT: s 61 LEU cc_start: 0.8212 (tp) cc_final: 0.7816 (tm) REVERT: s 79 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7037 (mp0) REVERT: s 121 MET cc_start: 0.7155 (ptp) cc_final: 0.6725 (pmm) REVERT: s 125 TYR cc_start: 0.6960 (m-80) cc_final: 0.6577 (m-80) REVERT: s 159 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7600 (tp) REVERT: s 197 SER cc_start: 0.8199 (t) cc_final: 0.7733 (t) REVERT: t 57 MET cc_start: 0.7172 (ttp) cc_final: 0.6869 (ttm) REVERT: t 86 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6841 (mm-30) REVERT: v 51 ASP cc_start: 0.7175 (m-30) cc_final: 0.6729 (t0) REVERT: v 55 LYS cc_start: 0.7384 (mtmt) cc_final: 0.6921 (ttmm) REVERT: v 79 ASP cc_start: 0.6318 (t0) cc_final: 0.5936 (t0) REVERT: v 87 GLN cc_start: 0.7671 (mp10) cc_final: 0.7202 (mm-40) REVERT: v 95 LYS cc_start: 0.6434 (tttt) cc_final: 0.6163 (ttmt) REVERT: v 100 GLU cc_start: 0.7324 (tt0) cc_final: 0.6579 (tt0) REVERT: v 132 LEU cc_start: 0.7220 (mt) cc_final: 0.6898 (mt) REVERT: v 133 HIS cc_start: 0.7904 (p-80) cc_final: 0.6982 (m170) REVERT: v 136 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6880 (mt-10) REVERT: v 146 LYS cc_start: 0.6566 (tttt) cc_final: 0.5838 (tttm) REVERT: w 56 ASN cc_start: 0.6477 (t0) cc_final: 0.6254 (t0) REVERT: w 71 ASP cc_start: 0.7676 (m-30) cc_final: 0.7380 (m-30) REVERT: x 13 ILE cc_start: 0.8722 (mm) cc_final: 0.8439 (mp) REVERT: x 19 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: x 26 GLN cc_start: 0.7938 (tt0) cc_final: 0.7714 (tm-30) REVERT: y 16 GLU cc_start: 0.6201 (mt-10) cc_final: 0.5993 (mt-10) REVERT: y 23 LYS cc_start: 0.7924 (mttt) cc_final: 0.7345 (mmmt) REVERT: y 38 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.5777 (mp0) REVERT: y 47 LYS cc_start: 0.6274 (ttpp) cc_final: 0.6023 (tttm) REVERT: y 48 SER cc_start: 0.7600 (t) cc_final: 0.7228 (p) REVERT: y 70 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7163 (ttmm) REVERT: z 25 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6160 (mp0) REVERT: z 35 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7571 (ttp80) REVERT: z 39 CYS cc_start: 0.6596 (OUTLIER) cc_final: 0.6369 (p) outliers start: 113 outliers final: 69 residues processed: 600 average time/residue: 1.6459 time to fit residues: 1173.9905 Evaluate side-chains 622 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 522 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 65 ILE Chi-restraints excluded: chain o residue 70 ARG Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 105 LYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 140 ARG Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 404 GLU Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 485 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 960 ARG Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1281 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1410 HIS Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 220 GLU Chi-restraints excluded: chain p residue 222 ARG Chi-restraints excluded: chain p residue 288 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 483 ARG Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 563 ASP Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 578 LYS Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 644 LYS Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 763 SER Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 118 ARG Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 34 ASP Chi-restraints excluded: chain s residue 86 THR Chi-restraints excluded: chain s residue 96 GLU Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain t residue 110 LEU Chi-restraints excluded: chain u residue 32 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 110 THR Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 39 CYS Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 3.9990 chunk 355 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 307 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1410 HIS ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 518 HIS p 582 GLN ** p 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 4 HIS u 28 GLN ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116365 restraints weight = 40915.716| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.03 r_work: 0.3122 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36597 Z= 0.343 Angle : 0.507 10.025 49911 Z= 0.269 Chirality : 0.042 0.177 5557 Planarity : 0.003 0.046 6097 Dihedral : 15.773 174.706 5807 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 27.87 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.25 % Favored : 94.56 % Rotamer: Outliers : 3.28 % Allowed : 19.71 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.63 (0.13), residues: 4137 helix: 1.76 (0.14), residues: 1406 sheet: 0.17 (0.20), residues: 644 loop : -0.40 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP q 49 HIS 0.016 0.001 HIS r 43 PHE 0.019 0.001 PHE q 63 TYR 0.017 0.002 TYR t 115 ARG 0.006 0.000 ARG q 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18453.40 seconds wall clock time: 324 minutes 54.83 seconds (19494.83 seconds total)