Starting phenix.real_space_refine on Sat Mar 23 05:40:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wax_37408/03_2024/8wax_37408_trim_updated.pdb" } resolution = 2.75 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= 0.112 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 22166 2.51 5 N 6279 2.21 5 O 6958 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 TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 206": "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 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35751 Number of models: 1 Model: "" Number of chains: 24 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: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 874 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1117 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 11} 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: "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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' ZN': 1, 'W0F': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 4739 SG CYS o 71 114.004 112.515 115.146 1.00141.57 S ATOM 4761 SG CYS o 74 111.780 115.464 115.171 1.00137.29 S ATOM 4808 SG CYS o 81 110.285 111.893 114.903 1.00138.71 S ATOM 5043 SG CYS o 111 101.546 111.251 68.275 1.00164.45 S ATOM 5071 SG CYS o 114 103.671 114.613 68.036 1.00163.67 S ATOM 5417 SG CYS o 184 103.737 111.994 65.226 1.00171.81 S ATOM 24504 SG CYS p1119 105.472 124.992 103.960 1.00141.59 S ATOM 24526 SG CYS p1122 105.446 121.788 101.845 1.00142.57 S ATOM 24641 SG CYS p1137 108.298 122.496 104.004 1.00148.67 S ATOM 24662 SG CYS p1140 107.802 124.286 100.695 1.00152.98 S ATOM 25628 SG CYS q 88 85.526 90.727 173.430 1.00138.12 S ATOM 25641 SG CYS q 90 88.974 89.834 172.316 1.00147.15 S ATOM 25676 SG CYS q 94 87.149 87.436 174.593 1.00132.97 S ATOM 25698 SG CYS q 97 85.794 87.745 171.174 1.00132.45 S ATOM 33004 SG CYS w 17 75.557 52.456 55.853 1.00161.53 S ATOM 33028 SG CYS w 20 78.938 53.571 57.337 1.00163.91 S ATOM 33189 SG CYS w 39 76.690 56.232 56.454 1.00169.29 S ATOM 33214 SG CYS w 42 78.031 54.041 53.641 1.00167.79 S ATOM 33566 SG CYS w 86 44.266 43.148 86.112 1.00150.39 S ATOM 33590 SG CYS w 89 44.857 39.713 87.848 1.00155.57 S ATOM 33794 SG CYS w 114 46.605 42.868 89.078 1.00146.35 S ATOM 33829 SG CYS w 119 47.396 41.288 85.640 1.00152.45 S ATOM 33939 SG CYS x 7 65.597 72.390 151.601 1.00 98.61 S ATOM 33963 SG CYS x 10 63.960 73.335 154.842 1.00 95.35 S ATOM 34227 SG CYS x 44 61.760 72.466 151.633 1.00107.46 S ATOM 34233 SG CYS x 45 63.287 70.122 154.022 1.00108.23 S ATOM 35379 SG CYS z 19 107.094 61.276 142.318 1.00146.64 S ATOM 35398 SG CYS z 22 108.001 58.746 144.846 1.00145.85 S ATOM 35515 SG CYS z 36 110.696 61.340 143.914 1.00153.01 S ATOM 35541 SG CYS z 39 109.495 58.912 141.276 1.00150.68 S Time building chain proxies: 19.08, per 1000 atoms: 0.53 Number of scatterers: 35751 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 6958 8.00 N 6279 7.00 C 22166 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.78 Conformation dependent library (CDL) restraints added in 6.4 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 p1202 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1122 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1137 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1140 " pdb="ZN ZN p1202 " - 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 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " 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: 143 helices and 44 sheets defined 32.6% alpha, 15.0% beta 39 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 15.67 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: 4.165A 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: 4.247A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.866A 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: 3.613A 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: 4.172A 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 540 through 548 Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.823A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.904A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.224A 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: 4.455A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.834A 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 971 through 973 No H-bonds generated for 'chain 'o' and resid 971 through 973' Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1019 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: 4.139A 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: 3.748A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.078A 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: 3.836A 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: 3.840A 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: 3.779A 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 708 through 710 No H-bonds generated for 'chain 'p' and resid 708 through 710' 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: 3.706A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 741 removed outlier: 4.631A pdb=" N HIS p 741 " --> pdb=" O THR p 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 738 through 741' 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: 3.560A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.861A 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: 4.131A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.596A 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 134 through 136 No H-bonds generated for 'chain 's' and resid 134 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 64 through 66 No H-bonds generated for 'chain 'w' and resid 64 through 66' Processing helix chain 'w' and resid 70 through 74 Processing helix chain 'x' and resid 15 through 27 removed outlier: 4.186A pdb=" N TRP x 18 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU x 19 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA x 20 " --> pdb=" O LYS x 17 " (cutoff:3.500A) Processing helix chain 'x' and resid 31 through 38 Processing helix chain 'x' and resid 43 through 50 removed outlier: 3.571A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.730A 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: 3.781A 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: 6.826A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.006A 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: 3.568A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.163A 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: 11.282A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.914A 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: 4.201A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.683A 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: 3.596A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.385A 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: 4.615A 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: 3.565A 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: 6.083A 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: 3.948A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.114A 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: 3.596A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.192A 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: 3.669A 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: 4.361A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.740A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.232A 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: 6.860A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.588A 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: 3.568A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.448A 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: 6.910A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.391A 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: 6.801A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.665A 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: 6.139A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 4.960A 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: 6.264A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 6.014A 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: 3.671A 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: 7.011A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER u 105 " --> pdb=" O ILE u 157 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.487A 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: 6.846A 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: 6.841A 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: 5.235A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.717A 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. 3234 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 17.20 Time building geometry restraints manager: 15.94 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: 10194 1.33 - 1.49: 11564 1.49 - 1.65: 14549 1.65 - 1.82: 325 Bond restraints: 36655 Sorted by residual: bond pdb=" C2' G2L Z 14 " pdb=" C1' G2L Z 14 " ideal model delta sigma weight residual 1.271 1.522 -0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C4' G2L Z 14 " pdb=" C3' G2L Z 14 " ideal model delta sigma weight residual 1.270 1.521 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" CA ILE o1486 " pdb=" CB ILE o1486 " ideal model delta sigma weight residual 1.539 1.485 0.054 5.40e-03 3.43e+04 9.90e+01 bond pdb=" C CYS r 104 " pdb=" O CYS r 104 " ideal model delta sigma weight residual 1.235 1.197 0.038 4.70e-03 4.53e+04 6.48e+01 bond pdb=" N ILE N 4 " pdb=" H ILE N 4 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 36650 not shown) Histogram of bond angle deviations from ideal: 75.37 - 88.75: 1 88.75 - 102.12: 269 102.12 - 115.49: 24108 115.49 - 128.86: 25346 128.86 - 142.24: 292 Bond angle restraints: 50016 Sorted by residual: angle pdb=" N09 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" O05 W0F p1201 " ideal model delta sigma weight residual 110.18 75.37 34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C07 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " ideal model delta sigma weight residual 110.46 136.28 -25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" P26 W0F p1201 " pdb=" O29 W0F p1201 " pdb=" P30 W0F p1201 " ideal model delta sigma weight residual 123.60 142.24 -18.64 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" C10 W0F p1201 " ideal model delta sigma weight residual 99.38 117.51 -18.13 3.00e+00 1.11e-01 3.65e+01 angle pdb=" C ASP p 355 " pdb=" CA ASP p 355 " pdb=" CB ASP p 355 " ideal model delta sigma weight residual 117.23 109.70 7.53 1.36e+00 5.41e-01 3.07e+01 ... (remaining 50011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 21133 30.81 - 61.63: 977 61.63 - 92.44: 34 92.44 - 123.26: 3 123.26 - 154.07: 1 Dihedral angle restraints: 22148 sinusoidal: 9988 harmonic: 12160 Sorted by residual: dihedral pdb=" O4' U Z 2 " pdb=" C1' U Z 2 " pdb=" N1 U Z 2 " pdb=" C2 U Z 2 " ideal model delta sinusoidal sigma weight residual -160.00 -42.26 -117.74 1 1.50e+01 4.44e-03 6.25e+01 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 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+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 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 22145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4893 0.074 - 0.149: 654 0.149 - 0.223: 17 0.223 - 0.297: 1 0.297 - 0.371: 3 Chirality restraints: 5568 Sorted by residual: chirality pdb=" C06 W0F p1201 " pdb=" C07 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" O05 W0F p1201 " both_signs ideal model delta sigma weight residual False 2.41 2.04 0.37 2.00e-01 2.50e+01 3.45e+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 3.09e+00 chirality pdb=" C03 W0F p1201 " pdb=" C04 W0F p1201 " pdb=" C07 W0F p1201 " pdb=" O02 W0F p1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 5565 not shown) Planarity restraints: 6103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F p1201 " -0.108 2.00e-02 2.50e+03 4.14e-02 5.13e+01 pdb=" C10 W0F p1201 " 0.040 2.00e-02 2.50e+03 pdb=" C12 W0F p1201 " 0.007 2.00e-02 2.50e+03 pdb=" C13 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" C15 W0F p1201 " 0.008 2.00e-02 2.50e+03 pdb=" C17 W0F p1201 " -0.019 2.00e-02 2.50e+03 pdb=" N09 W0F p1201 " 0.051 2.00e-02 2.50e+03 pdb=" N11 W0F p1201 " 0.013 2.00e-02 2.50e+03 pdb=" N14 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" N16 W0F p1201 " -0.018 2.00e-02 2.50e+03 pdb=" N19 W0F p1201 " 0.006 2.00e-02 2.50e+03 pdb=" O18 W0F p1201 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ILE p 51 " 0.075 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.025 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 4.06e-02 1.65e+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 6100 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 46 2.39 - 2.94: 15922 2.94 - 3.50: 41193 3.50 - 4.05: 70796 4.05 - 4.60: 102128 Nonbonded interactions: 230085 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.838 2.050 nonbonded pdb=" C10 W0F p1201 " pdb=" O05 W0F p1201 " model vdw 1.871 2.520 nonbonded pdb=" OD1 ASP o 497 " pdb="MG MG o2003 " model vdw 1.915 2.050 nonbonded pdb="HG22 ILE N 4 " pdb="HD13 ILE N 4 " model vdw 2.019 2.440 nonbonded pdb=" OD2 ASP o 497 " pdb=" O33 W0F p1201 " model vdw 2.050 2.800 ... (remaining 230080 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: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.890 Extract box with map and model: 8.590 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 110.090 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5325 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 0.251 36632 Z= 0.515 Angle : 0.783 34.806 49964 Z= 0.402 Chirality : 0.048 0.371 5568 Planarity : 0.005 0.078 6099 Dihedral : 15.323 154.071 14275 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.99 % Favored : 95.82 % Rotamer: Outliers : 1.25 % Allowed : 5.91 % Favored : 92.84 % 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: 0.46 (0.13), residues: 4137 helix: 1.28 (0.14), residues: 1413 sheet: 0.20 (0.20), residues: 673 loop : -0.27 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP o1192 HIS 0.007 0.001 HIS o 809 PHE 0.023 0.002 PHE q 93 TYR 0.033 0.002 TYR o 669 ARG 0.006 0.001 ARG q 67 *********************** 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 1020 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 974 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.7080 (mmt90) cc_final: 0.6607 (mmt-90) REVERT: o 18 ILE cc_start: 0.8416 (mt) cc_final: 0.8089 (mm) REVERT: o 19 LYS cc_start: 0.7025 (mttp) cc_final: 0.6537 (mmtm) REVERT: o 31 LEU cc_start: 0.7293 (mt) cc_final: 0.6903 (mt) REVERT: o 67 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7507 (ttp80) REVERT: o 78 MET cc_start: 0.7854 (tpp) cc_final: 0.7115 (tpp) REVERT: o 80 GLU cc_start: 0.5904 (tp30) cc_final: 0.5568 (tm-30) REVERT: o 197 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7542 (pt0) REVERT: o 219 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7058 (mp0) REVERT: o 272 ASN cc_start: 0.7708 (m-40) cc_final: 0.7256 (t0) REVERT: o 382 ARG cc_start: 0.5883 (mtp-110) cc_final: 0.5544 (ttm110) REVERT: o 426 ARG cc_start: 0.6943 (mtm180) cc_final: 0.6720 (ptp-110) REVERT: o 495 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.5670 (p0) REVERT: o 500 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8089 (mt-10) REVERT: o 514 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6423 (tt0) REVERT: o 524 MET cc_start: 0.8201 (mmp) cc_final: 0.7941 (mmt) REVERT: o 552 ASP cc_start: 0.6423 (m-30) cc_final: 0.6101 (m-30) REVERT: o 556 GLU cc_start: 0.6659 (pt0) cc_final: 0.5994 (tp30) REVERT: o 619 LYS cc_start: 0.6777 (mtpp) cc_final: 0.6499 (mttp) REVERT: o 634 GLU cc_start: 0.6847 (tt0) cc_final: 0.6267 (mt-10) REVERT: o 691 ASP cc_start: 0.7536 (m-30) cc_final: 0.7331 (m-30) REVERT: o 728 THR cc_start: 0.7806 (m) cc_final: 0.7244 (t) REVERT: o 803 LYS cc_start: 0.7445 (tttp) cc_final: 0.7201 (tptp) REVERT: o 818 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7187 (mp0) REVERT: o 841 MET cc_start: 0.6785 (mtp) cc_final: 0.6575 (mtm) REVERT: o 849 ASP cc_start: 0.5881 (m-30) cc_final: 0.5556 (m-30) REVERT: o 861 GLN cc_start: 0.7474 (tp40) cc_final: 0.6997 (mt0) REVERT: o 868 MET cc_start: 0.7502 (ptt) cc_final: 0.7106 (ptm) REVERT: o 900 SER cc_start: 0.8166 (m) cc_final: 0.7923 (t) REVERT: o 936 GLU cc_start: 0.7441 (tt0) cc_final: 0.7051 (tm-30) REVERT: o 1026 ASP cc_start: 0.7968 (t0) cc_final: 0.7720 (p0) REVERT: o 1063 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6144 (mt-10) REVERT: o 1085 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6449 (mm-30) REVERT: o 1136 THR cc_start: 0.8160 (m) cc_final: 0.7917 (p) REVERT: o 1167 ARG cc_start: 0.6967 (ttp-110) cc_final: 0.6759 (ttm-80) REVERT: o 1186 VAL cc_start: 0.7221 (t) cc_final: 0.6931 (t) REVERT: o 1229 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8400 (tp30) REVERT: o 1257 LEU cc_start: 0.6625 (tp) cc_final: 0.5988 (tm) REVERT: o 1262 MET cc_start: 0.6972 (ttt) cc_final: 0.6548 (tpp) REVERT: o 1306 LYS cc_start: 0.6590 (mttt) cc_final: 0.5916 (tttm) REVERT: o 1318 LYS cc_start: 0.6324 (mtpt) cc_final: 0.5733 (mtmt) REVERT: o 1321 ILE cc_start: 0.8088 (mt) cc_final: 0.7863 (pt) REVERT: o 1335 ILE cc_start: 0.6590 (pt) cc_final: 0.6390 (pt) REVERT: o 1337 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5948 (mt-10) REVERT: o 1339 ASP cc_start: 0.6502 (t0) cc_final: 0.6259 (m-30) REVERT: o 1361 ASP cc_start: 0.6713 (t0) cc_final: 0.6467 (t0) REVERT: o 1396 ARG cc_start: 0.6914 (mtt-85) cc_final: 0.6602 (mtt90) REVERT: o 1422 GLN cc_start: 0.7215 (mt0) cc_final: 0.5878 (mm-40) REVERT: o 1423 ASP cc_start: 0.8040 (m-30) cc_final: 0.7523 (t0) REVERT: o 1437 ASP cc_start: 0.7003 (m-30) cc_final: 0.6437 (t0) REVERT: o 1452 LYS cc_start: 0.7473 (mttt) cc_final: 0.6928 (mmtm) REVERT: o 1454 VAL cc_start: 0.7008 (t) cc_final: 0.6726 (t) REVERT: p 17 ILE cc_start: 0.8078 (mt) cc_final: 0.7769 (mm) REVERT: p 20 ASP cc_start: 0.5738 (m-30) cc_final: 0.5508 (p0) REVERT: p 53 MET cc_start: 0.5964 (mmm) cc_final: 0.5587 (mmm) REVERT: p 88 PHE cc_start: 0.7435 (m-80) cc_final: 0.7080 (m-80) REVERT: p 98 HIS cc_start: 0.7427 (t70) cc_final: 0.7213 (t-170) REVERT: p 128 ILE cc_start: 0.7161 (mt) cc_final: 0.6806 (mt) REVERT: p 144 HIS cc_start: 0.6103 (m-70) cc_final: 0.5811 (m170) REVERT: p 200 MET cc_start: 0.7477 (ttm) cc_final: 0.7218 (tpp) REVERT: p 234 THR cc_start: 0.8367 (p) cc_final: 0.8153 (t) REVERT: p 239 MET cc_start: 0.7071 (ttm) cc_final: 0.6837 (ttp) REVERT: p 240 LEU cc_start: 0.7557 (mt) cc_final: 0.7343 (mt) REVERT: p 254 GLN cc_start: 0.6397 (mt0) cc_final: 0.6044 (mp10) REVERT: p 292 PHE cc_start: 0.6095 (m-10) cc_final: 0.5650 (m-10) REVERT: p 307 GLU cc_start: 0.7882 (tp30) cc_final: 0.7518 (tp30) REVERT: p 313 GLU cc_start: 0.7201 (mt-10) cc_final: 0.7000 (tp30) REVERT: p 315 ASN cc_start: 0.7302 (m-40) cc_final: 0.7066 (m-40) REVERT: p 335 ARG cc_start: 0.7006 (mtm180) cc_final: 0.6799 (mtm180) REVERT: p 381 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7573 (mp0) REVERT: p 386 ASP cc_start: 0.7998 (m-30) cc_final: 0.7383 (m-30) REVERT: p 420 GLN cc_start: 0.6776 (tt0) cc_final: 0.6547 (tp40) REVERT: p 471 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7229 (t0) REVERT: p 486 ASN cc_start: 0.8353 (t0) cc_final: 0.7643 (t0) REVERT: p 551 GLU cc_start: 0.7692 (mp0) cc_final: 0.6983 (pm20) REVERT: p 574 VAL cc_start: 0.7981 (t) cc_final: 0.7774 (m) REVERT: p 577 HIS cc_start: 0.7494 (t-170) cc_final: 0.6906 (t70) REVERT: p 630 LYS cc_start: 0.6976 (mttt) cc_final: 0.6709 (mmtm) REVERT: p 683 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6258 (mm-40) REVERT: p 728 MET cc_start: 0.7038 (mtm) cc_final: 0.6789 (mtp) REVERT: p 737 ILE cc_start: 0.7734 (mt) cc_final: 0.7406 (tp) REVERT: p 796 MET cc_start: 0.8862 (mtm) cc_final: 0.8436 (mtm) REVERT: p 798 ARG cc_start: 0.6616 (ttt90) cc_final: 0.6149 (ttm-80) REVERT: p 802 ASP cc_start: 0.6554 (m-30) cc_final: 0.6284 (m-30) REVERT: p 817 GLN cc_start: 0.7304 (tt0) cc_final: 0.6610 (pm20) REVERT: p 897 ARG cc_start: 0.6619 (mmt90) cc_final: 0.6342 (mmt90) REVERT: p 1054 MET cc_start: 0.8161 (mtm) cc_final: 0.7758 (mtm) REVERT: p 1076 GLU cc_start: 0.7797 (tt0) cc_final: 0.7495 (tt0) REVERT: p 1080 ARG cc_start: 0.6913 (mtt90) cc_final: 0.6383 (mmp-170) REVERT: p 1101 GLN cc_start: 0.7389 (tt0) cc_final: 0.6908 (tt0) REVERT: p 1151 MET cc_start: 0.7582 (ptm) cc_final: 0.7319 (ptm) REVERT: p 1165 MET cc_start: 0.7686 (mtm) cc_final: 0.7160 (mtp) REVERT: p 1172 MET cc_start: 0.7275 (mmt) cc_final: 0.6811 (mmt) REVERT: q 17 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6837 (pm20) REVERT: q 81 LYS cc_start: 0.7322 (mtpt) cc_final: 0.6889 (mttt) REVERT: q 93 PHE cc_start: 0.7775 (m-80) cc_final: 0.6738 (m-80) REVERT: q 106 ARG cc_start: 0.7343 (ttt180) cc_final: 0.7045 (ttm-80) REVERT: q 108 ASN cc_start: 0.7112 (m-40) cc_final: 0.6641 (m-40) REVERT: q 121 ILE cc_start: 0.7968 (mt) cc_final: 0.7754 (mm) REVERT: q 126 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6403 (mtp85) REVERT: q 199 LYS cc_start: 0.7929 (mttt) cc_final: 0.7501 (mtmm) REVERT: q 225 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7731 (ttpp) REVERT: q 254 LYS cc_start: 0.6018 (tttt) cc_final: 0.5682 (mppt) REVERT: s 33 LEU cc_start: 0.7154 (tt) cc_final: 0.6905 (tp) REVERT: s 120 ASP cc_start: 0.8350 (m-30) cc_final: 0.8073 (m-30) REVERT: s 126 ILE cc_start: 0.7785 (mt) cc_final: 0.7518 (mp) REVERT: s 137 ILE cc_start: 0.7540 (mt) cc_final: 0.7008 (pp) REVERT: s 158 GLU cc_start: 0.6170 (tt0) cc_final: 0.5853 (pt0) REVERT: s 167 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6761 (mp0) REVERT: s 210 GLN cc_start: 0.6377 (mt0) cc_final: 0.6144 (mm-40) REVERT: t 57 MET cc_start: 0.7427 (ttp) cc_final: 0.7126 (ttm) REVERT: t 79 VAL cc_start: 0.7195 (t) cc_final: 0.6211 (p) REVERT: t 80 MET cc_start: 0.7725 (mmt) cc_final: 0.6401 (mpt) REVERT: t 82 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8099 (pm20) REVERT: t 86 GLU cc_start: 0.6361 (mm-30) cc_final: 0.5842 (mm-30) REVERT: t 102 ILE cc_start: 0.7734 (mt) cc_final: 0.7523 (mt) REVERT: t 115 TYR cc_start: 0.8035 (p90) cc_final: 0.7801 (p90) REVERT: t 116 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7593 (mt-10) REVERT: u 1 MET cc_start: 0.8230 (tpp) cc_final: 0.7722 (tmt) REVERT: u 29 LYS cc_start: 0.5088 (mmtt) cc_final: 0.4759 (mmmt) REVERT: u 44 PHE cc_start: 0.8411 (m-80) cc_final: 0.7325 (m-10) REVERT: u 76 VAL cc_start: 0.7557 (m) cc_final: 0.7261 (p) REVERT: u 77 PHE cc_start: 0.5542 (t80) cc_final: 0.5306 (t80) REVERT: u 104 MET cc_start: 0.7392 (ttp) cc_final: 0.6898 (tpp) REVERT: u 165 ASP cc_start: 0.6973 (m-30) cc_final: 0.6721 (t70) REVERT: v 21 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7699 (mmtm) REVERT: v 37 MET cc_start: 0.7716 (mtp) cc_final: 0.7398 (mtp) REVERT: v 51 ASP cc_start: 0.7426 (m-30) cc_final: 0.7001 (p0) REVERT: v 58 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7238 (tp) REVERT: v 63 THR cc_start: 0.8606 (p) cc_final: 0.8105 (t) REVERT: v 76 ASN cc_start: 0.7622 (m-40) cc_final: 0.7199 (m-40) REVERT: v 100 GLU cc_start: 0.6933 (tt0) cc_final: 0.6722 (tt0) REVERT: v 126 GLN cc_start: 0.7644 (tt0) cc_final: 0.7273 (tt0) REVERT: v 136 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7203 (pt0) REVERT: v 146 LYS cc_start: 0.6708 (tttt) cc_final: 0.6394 (tttm) REVERT: w 44 TYR cc_start: 0.7784 (t80) cc_final: 0.7495 (t80) REVERT: w 71 ASP cc_start: 0.7745 (m-30) cc_final: 0.7195 (m-30) REVERT: w 108 MET cc_start: 0.7651 (mtp) cc_final: 0.7418 (mtp) REVERT: x 26 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6654 (pt0) REVERT: y 8 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7223 (mt-10) REVERT: y 23 LYS cc_start: 0.8162 (mttt) cc_final: 0.7792 (mtpm) REVERT: y 32 LEU cc_start: 0.7302 (tp) cc_final: 0.6968 (mt) REVERT: y 37 LYS cc_start: 0.7462 (mmtm) cc_final: 0.7248 (mmmm) REVERT: y 39 ASP cc_start: 0.6462 (p0) cc_final: 0.6126 (p0) REVERT: y 48 SER cc_start: 0.7928 (t) cc_final: 0.7665 (p) REVERT: y 85 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5949 (tt0) REVERT: z 15 MET cc_start: 0.5910 (mmm) cc_final: 0.5400 (mpp) REVERT: z 16 ILE cc_start: 0.7861 (mt) cc_final: 0.7656 (mt) REVERT: z 26 ASN cc_start: 0.6088 (p0) cc_final: 0.5727 (p0) REVERT: z 42 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7567 (mtt90) outliers start: 46 outliers final: 11 residues processed: 1007 average time/residue: 1.6657 time to fit residues: 1971.8682 Evaluate side-chains 637 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 623 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 367 ILE Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 541 ILE Chi-restraints excluded: chain u residue 156 ASP Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain x residue 16 ASN 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: 8.9990 chunk 177 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 329 optimal weight: 40.0000 chunk 127 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 chunk 382 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 178 GLN o 181 HIS ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 516 GLN o 531 ASN o 539 GLN o 671 ASN ** o 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** o1024 ASN ** o1044 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS o1310 HIS o1445 HIS o1462 GLN p 43 GLN p 56 GLN p 117 ASN p 164 ASN p 245 GLN p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 639 HIS p 649 ASN p 699 HIS ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 838 GLN p 941 GLN p 948 GLN p1068 GLN p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 HIS r 66 ASN r 129 GLN s 64 HIS s 133 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 53 ASN v 44 ASN v 133 HIS w 50 ASN w 74 GLN w 98 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36632 Z= 0.203 Angle : 0.489 10.455 49964 Z= 0.264 Chirality : 0.041 0.170 5568 Planarity : 0.003 0.057 6099 Dihedral : 16.791 150.673 5845 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 3.74 % Allowed : 14.56 % Favored : 81.70 % 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: 0.92 (0.13), residues: 4137 helix: 1.86 (0.14), residues: 1400 sheet: 0.28 (0.20), residues: 675 loop : -0.09 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP o 679 HIS 0.011 0.001 HIS r 43 PHE 0.021 0.001 PHE p 356 TYR 0.020 0.001 TYR q 231 ARG 0.015 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 769 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 631 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.7064 (mmt90) cc_final: 0.6511 (mmt-90) REVERT: o 18 ILE cc_start: 0.8342 (mt) cc_final: 0.8127 (mm) REVERT: o 66 GLU cc_start: 0.7914 (pm20) cc_final: 0.7676 (pm20) REVERT: o 116 LYS cc_start: 0.6907 (mttt) cc_final: 0.6420 (mtmm) REVERT: o 138 LYS cc_start: 0.6379 (tttm) cc_final: 0.6153 (ttmm) REVERT: o 192 ARG cc_start: 0.7469 (ptm-80) cc_final: 0.7108 (ptm160) REVERT: o 197 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7492 (pt0) REVERT: o 201 GLU cc_start: 0.6270 (tt0) cc_final: 0.5889 (pt0) REVERT: o 219 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6876 (mp0) REVERT: o 227 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6704 (mtm-85) REVERT: o 233 CYS cc_start: 0.6091 (t) cc_final: 0.5769 (p) REVERT: o 238 MET cc_start: 0.7425 (mtt) cc_final: 0.6872 (mtp) REVERT: o 272 ASN cc_start: 0.7739 (m-40) cc_final: 0.7414 (t0) REVERT: o 311 GLN cc_start: 0.7567 (tp40) cc_final: 0.7150 (tp40) REVERT: o 382 ARG cc_start: 0.6231 (mtp-110) cc_final: 0.5835 (ttm110) REVERT: o 426 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6771 (ptp-110) REVERT: o 495 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5477 (p0) REVERT: o 514 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6351 (tt0) REVERT: o 524 MET cc_start: 0.8186 (mmp) cc_final: 0.7327 (mmm) REVERT: o 580 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7296 (mt) REVERT: o 612 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6599 (p0) REVERT: o 619 LYS cc_start: 0.6794 (mtpp) cc_final: 0.6428 (mttp) REVERT: o 634 GLU cc_start: 0.6961 (tt0) cc_final: 0.6302 (mt-10) REVERT: o 691 ASP cc_start: 0.7708 (m-30) cc_final: 0.7487 (m-30) REVERT: o 728 THR cc_start: 0.7793 (m) cc_final: 0.7327 (t) REVERT: o 803 LYS cc_start: 0.7425 (tttp) cc_final: 0.7201 (tptp) REVERT: o 818 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7229 (mp0) REVERT: o 841 MET cc_start: 0.6619 (mtp) cc_final: 0.6383 (mtm) REVERT: o 845 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5999 (tt0) REVERT: o 861 GLN cc_start: 0.7268 (tp40) cc_final: 0.6604 (mt0) REVERT: o 868 MET cc_start: 0.7505 (ptt) cc_final: 0.7147 (ptm) REVERT: o 900 SER cc_start: 0.8200 (m) cc_final: 0.7922 (t) REVERT: o 909 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.7006 (tt) REVERT: o 936 GLU cc_start: 0.7292 (tt0) cc_final: 0.6868 (tm-30) REVERT: o 1063 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6409 (mt-10) REVERT: o 1085 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6398 (mm-30) REVERT: o 1136 THR cc_start: 0.8318 (m) cc_final: 0.8086 (t) REVERT: o 1229 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8536 (tp30) REVERT: o 1262 MET cc_start: 0.6904 (ttt) cc_final: 0.6552 (tpp) REVERT: o 1269 MET cc_start: 0.3317 (OUTLIER) cc_final: 0.2906 (pmm) REVERT: o 1286 ARG cc_start: 0.7219 (ttm-80) cc_final: 0.6706 (mtp85) REVERT: o 1306 LYS cc_start: 0.6285 (mttt) cc_final: 0.5658 (tttm) REVERT: o 1318 LYS cc_start: 0.6144 (mtpt) cc_final: 0.5495 (mtmt) REVERT: o 1321 ILE cc_start: 0.8164 (mt) cc_final: 0.7946 (pt) REVERT: o 1337 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5966 (mt-10) REVERT: o 1361 ASP cc_start: 0.6859 (t0) cc_final: 0.6555 (t0) REVERT: o 1422 GLN cc_start: 0.7131 (mt0) cc_final: 0.5789 (mm110) REVERT: o 1423 ASP cc_start: 0.8104 (m-30) cc_final: 0.7638 (t0) REVERT: o 1452 LYS cc_start: 0.7534 (mttt) cc_final: 0.6905 (mmtm) REVERT: o 1479 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.4832 (mtmt) REVERT: p 16 GLU cc_start: 0.5448 (pm20) cc_final: 0.5213 (pm20) REVERT: p 49 GLU cc_start: 0.6502 (tp30) cc_final: 0.6133 (tp30) REVERT: p 53 MET cc_start: 0.6147 (mmm) cc_final: 0.5783 (mmm) REVERT: p 117 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7726 (m-40) REVERT: p 222 ARG cc_start: 0.6419 (mtp-110) cc_final: 0.6003 (mtp85) REVERT: p 239 MET cc_start: 0.6853 (ttm) cc_final: 0.6618 (ttm) REVERT: p 240 LEU cc_start: 0.7500 (mt) cc_final: 0.7184 (mm) REVERT: p 254 GLN cc_start: 0.6257 (mt0) cc_final: 0.5964 (mp10) REVERT: p 324 ARG cc_start: 0.7425 (mtt90) cc_final: 0.6725 (mmm-85) REVERT: p 335 ARG cc_start: 0.6864 (mtm180) cc_final: 0.6131 (mtm-85) REVERT: p 381 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7540 (mp0) REVERT: p 385 ARG cc_start: 0.6856 (ttm110) cc_final: 0.5909 (ttm-80) REVERT: p 386 ASP cc_start: 0.7973 (m-30) cc_final: 0.7356 (m-30) REVERT: p 420 GLN cc_start: 0.6606 (tt0) cc_final: 0.6380 (tp40) REVERT: p 471 ASN cc_start: 0.7817 (OUTLIER) cc_final: 0.7262 (t0) REVERT: p 486 ASN cc_start: 0.8283 (t0) cc_final: 0.7624 (t0) REVERT: p 508 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.5620 (mtt) REVERT: p 551 GLU cc_start: 0.7611 (mp0) cc_final: 0.6640 (pm20) REVERT: p 563 ASP cc_start: 0.3880 (t0) cc_final: 0.3674 (t0) REVERT: p 576 ILE cc_start: 0.7777 (pt) cc_final: 0.6929 (pp) REVERT: p 597 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6591 (mm) REVERT: p 606 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6126 (t0) REVERT: p 630 LYS cc_start: 0.7099 (mttt) cc_final: 0.6678 (mmtm) REVERT: p 683 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6359 (mm-40) REVERT: p 728 MET cc_start: 0.7113 (mtm) cc_final: 0.6562 (mtp) REVERT: p 733 MET cc_start: 0.8113 (ttm) cc_final: 0.7854 (ttm) REVERT: p 739 ASN cc_start: 0.7700 (p0) cc_final: 0.7348 (p0) REVERT: p 771 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: p 796 MET cc_start: 0.8894 (mtm) cc_final: 0.8454 (mtm) REVERT: p 798 ARG cc_start: 0.6471 (ttt90) cc_final: 0.6175 (tpt170) REVERT: p 817 GLN cc_start: 0.7489 (tt0) cc_final: 0.6665 (pm20) REVERT: p 931 ILE cc_start: 0.7808 (pt) cc_final: 0.7450 (pp) REVERT: p 1054 MET cc_start: 0.8402 (mtm) cc_final: 0.7803 (mtm) REVERT: p 1080 ARG cc_start: 0.7021 (mtt90) cc_final: 0.6406 (mtp85) REVERT: p 1091 ARG cc_start: 0.5637 (OUTLIER) cc_final: 0.5016 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7586 (tp40) cc_final: 0.7033 (tt0) REVERT: p 1147 SER cc_start: 0.8347 (m) cc_final: 0.7863 (m) REVERT: p 1151 MET cc_start: 0.7582 (ptm) cc_final: 0.7320 (ptm) REVERT: p 1165 MET cc_start: 0.7803 (mtm) cc_final: 0.7418 (mtp) REVERT: p 1172 MET cc_start: 0.7309 (mmt) cc_final: 0.6639 (mmt) REVERT: q 17 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6777 (pm20) REVERT: q 41 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6626 (mt-10) REVERT: q 81 LYS cc_start: 0.7306 (mtpt) cc_final: 0.6845 (mttt) REVERT: q 106 ARG cc_start: 0.7426 (ttt180) cc_final: 0.7186 (ttm-80) REVERT: q 108 ASN cc_start: 0.7240 (m-40) cc_final: 0.6875 (m-40) REVERT: q 126 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6570 (mmp-170) REVERT: q 158 GLU cc_start: 0.7087 (tt0) cc_final: 0.6303 (pt0) REVERT: q 199 LYS cc_start: 0.8094 (mttt) cc_final: 0.7537 (mtmm) REVERT: q 254 LYS cc_start: 0.6140 (tttt) cc_final: 0.5783 (mppt) REVERT: s 108 GLN cc_start: 0.7493 (mt0) cc_final: 0.7085 (tt0) REVERT: s 125 TYR cc_start: 0.7105 (m-80) cc_final: 0.6693 (m-80) REVERT: s 126 ILE cc_start: 0.7667 (mt) cc_final: 0.7421 (mp) REVERT: s 137 ILE cc_start: 0.7776 (mt) cc_final: 0.7524 (pp) REVERT: s 158 GLU cc_start: 0.6314 (tt0) cc_final: 0.5959 (pt0) REVERT: s 167 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6843 (mp0) REVERT: s 172 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6962 (mtp85) REVERT: t 57 MET cc_start: 0.7662 (ttp) cc_final: 0.7264 (ttm) REVERT: t 80 MET cc_start: 0.6683 (mmt) cc_final: 0.6271 (mpt) REVERT: t 86 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5803 (mm-30) REVERT: t 95 LYS cc_start: 0.6343 (ttmm) cc_final: 0.6048 (mtpp) REVERT: t 116 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7381 (mt-10) REVERT: u 1 MET cc_start: 0.8064 (tpp) cc_final: 0.7711 (tmt) REVERT: u 16 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6262 (ptp-170) REVERT: u 44 PHE cc_start: 0.8815 (m-80) cc_final: 0.8218 (m-10) REVERT: u 53 ASN cc_start: 0.7613 (t0) cc_final: 0.7387 (t0) REVERT: u 76 VAL cc_start: 0.7675 (m) cc_final: 0.7426 (m) REVERT: u 77 PHE cc_start: 0.5640 (t80) cc_final: 0.5352 (t80) REVERT: u 104 MET cc_start: 0.7500 (ttp) cc_final: 0.7152 (tpp) REVERT: u 156 ASP cc_start: 0.9013 (t0) cc_final: 0.7920 (m-30) REVERT: u 166 ASP cc_start: 0.8509 (p0) cc_final: 0.8133 (p0) REVERT: v 20 LYS cc_start: 0.7280 (tttt) cc_final: 0.6991 (tptp) REVERT: v 21 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7699 (mmtm) REVERT: v 33 GLU cc_start: 0.5311 (mt-10) cc_final: 0.5103 (mt-10) REVERT: v 36 LYS cc_start: 0.6166 (mmtp) cc_final: 0.5577 (mmtm) REVERT: v 37 MET cc_start: 0.7754 (mtp) cc_final: 0.7369 (mtp) REVERT: v 51 ASP cc_start: 0.7752 (m-30) cc_final: 0.7340 (p0) REVERT: v 63 THR cc_start: 0.8543 (p) cc_final: 0.8124 (t) REVERT: v 76 ASN cc_start: 0.7621 (m-40) cc_final: 0.7414 (t0) REVERT: v 126 GLN cc_start: 0.7575 (tt0) cc_final: 0.7196 (tt0) REVERT: v 136 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7003 (pt0) REVERT: v 146 LYS cc_start: 0.6708 (tttt) cc_final: 0.6290 (tttm) REVERT: w 44 TYR cc_start: 0.7782 (t80) cc_final: 0.7490 (t80) REVERT: w 71 ASP cc_start: 0.7487 (m-30) cc_final: 0.7202 (m-30) REVERT: w 81 THR cc_start: 0.7639 (OUTLIER) cc_final: 0.7421 (t) REVERT: x 19 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: x 26 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6536 (pt0) REVERT: y 8 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7082 (mt-10) REVERT: y 23 LYS cc_start: 0.8112 (mttt) cc_final: 0.7890 (ttpp) REVERT: y 35 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7348 (mm) REVERT: y 37 LYS cc_start: 0.7691 (mmtm) cc_final: 0.7386 (mmtp) REVERT: y 47 LYS cc_start: 0.6666 (ttpp) cc_final: 0.6327 (tttm) REVERT: y 48 SER cc_start: 0.7937 (t) cc_final: 0.7683 (p) REVERT: y 84 GLN cc_start: 0.6724 (mp10) cc_final: 0.6228 (mp-120) REVERT: y 85 GLU cc_start: 0.6268 (mt-10) cc_final: 0.5715 (tt0) REVERT: z 15 MET cc_start: 0.6086 (mmm) cc_final: 0.5632 (mmt) REVERT: z 27 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6704 (tp30) REVERT: z 44 MET cc_start: 0.7973 (mmt) cc_final: 0.7701 (mmm) outliers start: 138 outliers final: 62 residues processed: 714 average time/residue: 1.5999 time to fit residues: 1354.5097 Evaluate side-chains 643 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 560 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 227 ARG Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 924 TYR Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1221 MET Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain o residue 1479 LYS Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 117 ASN Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 415 VAL Chi-restraints excluded: chain p residue 421 LYS Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 529 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 861 SER Chi-restraints excluded: chain p residue 896 LEU Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1069 ILE Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain p residue 1164 SER Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain s residue 172 ARG Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 81 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 52 LYS Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 318 optimal weight: 0.1980 chunk 260 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 383 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 379 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 307 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 485 ASN o 516 GLN ** o 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1093 GLN o1101 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS o1445 HIS p 56 GLN p 111 ASN p 144 HIS p 265 GLN p 312 GLN p 315 ASN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 486 ASN p 577 HIS ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 980 HIS p1021 HIS ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 38 HIS ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN u 60 GLN v 133 HIS w 50 ASN z 23 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 36632 Z= 0.310 Angle : 0.536 11.249 49964 Z= 0.285 Chirality : 0.042 0.184 5568 Planarity : 0.004 0.050 6099 Dihedral : 16.589 149.634 5827 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 4.77 % Allowed : 16.05 % Favored : 79.18 % 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: 0.71 (0.13), residues: 4137 helix: 1.67 (0.14), residues: 1402 sheet: 0.13 (0.19), residues: 685 loop : -0.18 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 479 HIS 0.016 0.002 HIS r 43 PHE 0.018 0.002 PHE q 63 TYR 0.027 0.002 TYR q 231 ARG 0.007 0.000 ARG p 463 *********************** 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 766 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 590 time to evaluate : 4.201 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: 0.7015 (mmt90) cc_final: 0.6413 (mmt-90) REVERT: o 116 LYS cc_start: 0.7587 (mttt) cc_final: 0.6952 (mtmm) REVERT: o 138 LYS cc_start: 0.6390 (tttm) cc_final: 0.6147 (ttmm) REVERT: o 192 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.7125 (ptm160) REVERT: o 197 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7663 (pt0) REVERT: o 201 GLU cc_start: 0.6284 (tt0) cc_final: 0.5903 (pt0) REVERT: o 219 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6865 (mp0) REVERT: o 227 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6576 (mtm-85) REVERT: o 233 CYS cc_start: 0.6098 (t) cc_final: 0.5833 (p) REVERT: o 238 MET cc_start: 0.7557 (mtt) cc_final: 0.7070 (mtp) REVERT: o 272 ASN cc_start: 0.8000 (m-40) cc_final: 0.7671 (t0) REVERT: o 305 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6895 (mm-30) REVERT: o 382 ARG cc_start: 0.6377 (mtp-110) cc_final: 0.6130 (ttm110) REVERT: o 426 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6817 (ptp-110) REVERT: o 514 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6296 (tt0) REVERT: o 524 MET cc_start: 0.8043 (mmp) cc_final: 0.7580 (mmm) REVERT: o 580 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7283 (mt) REVERT: o 612 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6713 (p0) REVERT: o 619 LYS cc_start: 0.6829 (mtpp) cc_final: 0.6459 (mttp) REVERT: o 634 GLU cc_start: 0.7127 (tt0) cc_final: 0.6520 (mt-10) REVERT: o 691 ASP cc_start: 0.7848 (m-30) cc_final: 0.7638 (m-30) REVERT: o 726 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: o 728 THR cc_start: 0.7964 (m) cc_final: 0.7448 (t) REVERT: o 803 LYS cc_start: 0.7595 (tttp) cc_final: 0.7289 (tptp) REVERT: o 818 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7339 (mp0) REVERT: o 861 GLN cc_start: 0.7280 (tp40) cc_final: 0.6629 (mt0) REVERT: o 868 MET cc_start: 0.7547 (ptt) cc_final: 0.7336 (ptt) REVERT: o 876 ASP cc_start: 0.7335 (t0) cc_final: 0.6367 (t0) REVERT: o 899 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: o 900 SER cc_start: 0.8222 (m) cc_final: 0.8005 (t) REVERT: o 936 GLU cc_start: 0.7669 (tt0) cc_final: 0.7385 (tp30) REVERT: o 957 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6773 (mm-30) REVERT: o 1063 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6566 (mt-10) REVERT: o 1085 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6335 (mm-30) REVERT: o 1104 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5401 (mm) REVERT: o 1107 PHE cc_start: 0.6198 (m-80) cc_final: 0.5928 (m-10) REVERT: o 1136 THR cc_start: 0.8279 (m) cc_final: 0.7965 (p) REVERT: o 1222 THR cc_start: 0.8603 (t) cc_final: 0.8182 (p) REVERT: o 1229 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8508 (tp30) REVERT: o 1262 MET cc_start: 0.7060 (ttt) cc_final: 0.6621 (tpp) REVERT: o 1286 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6758 (mtp85) REVERT: o 1306 LYS cc_start: 0.6130 (mttt) cc_final: 0.5556 (tttm) REVERT: o 1318 LYS cc_start: 0.5994 (mtpt) cc_final: 0.5265 (mtmt) REVERT: o 1337 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5943 (mt-10) REVERT: o 1361 ASP cc_start: 0.7402 (t0) cc_final: 0.7127 (t0) REVERT: o 1412 MET cc_start: 0.7248 (ttp) cc_final: 0.6743 (tmm) REVERT: o 1422 GLN cc_start: 0.6731 (mt0) cc_final: 0.5746 (mm-40) REVERT: o 1423 ASP cc_start: 0.8066 (m-30) cc_final: 0.7585 (t0) REVERT: o 1452 LYS cc_start: 0.7641 (mttt) cc_final: 0.6852 (mmtm) REVERT: o 1479 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5396 (mptp) REVERT: p 49 GLU cc_start: 0.6359 (tp30) cc_final: 0.6009 (tp30) REVERT: p 53 MET cc_start: 0.6405 (mmm) cc_final: 0.5749 (mmm) REVERT: p 57 ARG cc_start: 0.5172 (ttp-110) cc_final: 0.4810 (mtm110) REVERT: p 168 ASP cc_start: 0.5724 (p0) cc_final: 0.5453 (m-30) REVERT: p 222 ARG cc_start: 0.6160 (mtp-110) cc_final: 0.5900 (mtt180) REVERT: p 239 MET cc_start: 0.6864 (ttm) cc_final: 0.6557 (ttp) REVERT: p 240 LEU cc_start: 0.7545 (mt) cc_final: 0.7286 (mm) REVERT: p 254 GLN cc_start: 0.6635 (mt0) cc_final: 0.6298 (mp10) REVERT: p 298 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7458 (mmm) REVERT: p 324 ARG cc_start: 0.7359 (mtt90) cc_final: 0.6984 (mmm-85) REVERT: p 334 LYS cc_start: 0.7938 (tttt) cc_final: 0.7568 (tptt) REVERT: p 335 ARG cc_start: 0.6773 (mtm180) cc_final: 0.5988 (mtm-85) REVERT: p 381 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7556 (mp0) REVERT: p 385 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6032 (ttm-80) REVERT: p 386 ASP cc_start: 0.8090 (m-30) cc_final: 0.7324 (m-30) REVERT: p 508 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6548 (mtt) REVERT: p 551 GLU cc_start: 0.7552 (mp0) cc_final: 0.6795 (pm20) REVERT: p 556 ILE cc_start: 0.5246 (OUTLIER) cc_final: 0.4913 (mm) REVERT: p 563 ASP cc_start: 0.4256 (OUTLIER) cc_final: 0.3928 (t0) REVERT: p 576 ILE cc_start: 0.7789 (pt) cc_final: 0.6017 (pp) REVERT: p 597 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7548 (mm) REVERT: p 606 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6427 (t0) REVERT: p 630 LYS cc_start: 0.7226 (mttt) cc_final: 0.6764 (mmtm) REVERT: p 683 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6740 (mm110) REVERT: p 728 MET cc_start: 0.7210 (mtm) cc_final: 0.6752 (mtp) REVERT: p 745 ASP cc_start: 0.7550 (m-30) cc_final: 0.7272 (m-30) REVERT: p 771 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: p 796 MET cc_start: 0.8891 (mtm) cc_final: 0.8379 (mtm) REVERT: p 817 GLN cc_start: 0.7637 (tt0) cc_final: 0.6748 (pm20) REVERT: p 1054 MET cc_start: 0.8389 (mtm) cc_final: 0.7871 (mtm) REVERT: p 1080 ARG cc_start: 0.7060 (mtt90) cc_final: 0.6388 (mtp85) REVERT: p 1088 GLU cc_start: 0.6042 (mt-10) cc_final: 0.5799 (mt-10) REVERT: p 1091 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.5078 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7659 (tp40) cc_final: 0.7086 (tt0) REVERT: p 1147 SER cc_start: 0.8444 (m) cc_final: 0.8027 (m) REVERT: p 1165 MET cc_start: 0.7970 (mtm) cc_final: 0.7560 (mtp) REVERT: p 1172 MET cc_start: 0.7480 (mmt) cc_final: 0.7141 (mmt) REVERT: q 17 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6846 (pm20) REVERT: q 81 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7093 (mttt) REVERT: q 106 ARG cc_start: 0.7710 (ttt180) cc_final: 0.7319 (ttm-80) REVERT: q 126 ARG cc_start: 0.7763 (mtt180) cc_final: 0.6747 (mtp180) REVERT: q 158 GLU cc_start: 0.7271 (tt0) cc_final: 0.6466 (pt0) REVERT: q 199 LYS cc_start: 0.8077 (mttt) cc_final: 0.7566 (mtmm) REVERT: q 254 LYS cc_start: 0.6191 (tttt) cc_final: 0.5852 (mppt) REVERT: s 3 ASP cc_start: 0.5492 (m-30) cc_final: 0.5060 (t0) REVERT: s 104 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6227 (mm) REVERT: s 108 GLN cc_start: 0.7845 (mt0) cc_final: 0.7440 (tt0) REVERT: s 126 ILE cc_start: 0.7573 (mt) cc_final: 0.7312 (mp) REVERT: s 158 GLU cc_start: 0.6372 (tt0) cc_final: 0.6009 (pt0) REVERT: s 167 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6695 (mp0) REVERT: s 187 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6715 (ttt90) REVERT: t 57 MET cc_start: 0.7780 (ttp) cc_final: 0.7331 (ttm) REVERT: t 86 GLU cc_start: 0.6185 (mm-30) cc_final: 0.5657 (mm-30) REVERT: t 95 LYS cc_start: 0.6297 (ttmm) cc_final: 0.6028 (mtpp) REVERT: u 16 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6324 (ptp-170) REVERT: u 24 ASN cc_start: 0.6107 (t0) cc_final: 0.5897 (t0) REVERT: u 101 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7346 (pp) REVERT: u 104 MET cc_start: 0.7472 (ttp) cc_final: 0.6604 (tmm) REVERT: u 165 ASP cc_start: 0.6034 (t0) cc_final: 0.5827 (t0) REVERT: v 20 LYS cc_start: 0.7431 (tttt) cc_final: 0.7170 (mmmm) REVERT: v 36 LYS cc_start: 0.6273 (mmtp) cc_final: 0.6009 (mmtm) REVERT: v 37 MET cc_start: 0.7683 (mtp) cc_final: 0.7450 (mtp) REVERT: v 51 ASP cc_start: 0.7633 (m-30) cc_final: 0.7031 (p0) REVERT: v 63 THR cc_start: 0.8442 (p) cc_final: 0.8049 (t) REVERT: v 100 GLU cc_start: 0.6733 (tt0) cc_final: 0.5998 (mt-10) REVERT: v 126 GLN cc_start: 0.7432 (tt0) cc_final: 0.7072 (tt0) REVERT: v 136 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6889 (pt0) REVERT: v 146 LYS cc_start: 0.6709 (tttt) cc_final: 0.6245 (tttm) REVERT: w 71 ASP cc_start: 0.7758 (m-30) cc_final: 0.7458 (m-30) REVERT: x 19 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: y 23 LYS cc_start: 0.8181 (mttt) cc_final: 0.7754 (ttpp) REVERT: y 35 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7215 (mm) REVERT: y 47 LYS cc_start: 0.6782 (ttpp) cc_final: 0.6419 (tttm) REVERT: y 48 SER cc_start: 0.8011 (t) cc_final: 0.7716 (p) REVERT: y 84 GLN cc_start: 0.6852 (mp10) cc_final: 0.6461 (mp-120) REVERT: y 85 GLU cc_start: 0.6356 (mt-10) cc_final: 0.5727 (tt0) REVERT: y 110 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7022 (tttm) REVERT: z 15 MET cc_start: 0.6347 (mmm) cc_final: 0.5970 (mmt) REVERT: z 16 ILE cc_start: 0.7985 (mt) cc_final: 0.7555 (mp) REVERT: z 27 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6735 (tp30) REVERT: z 35 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7370 (ttm-80) REVERT: z 38 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: z 42 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.6942 (ttm110) REVERT: z 58 ARG cc_start: 0.6050 (mtt180) cc_final: 0.5837 (mtt180) outliers start: 176 outliers final: 78 residues processed: 695 average time/residue: 1.6239 time to fit residues: 1345.2772 Evaluate side-chains 663 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 562 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 191 ILE Chi-restraints excluded: chain o residue 227 ARG Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 726 GLU Chi-restraints excluded: chain o residue 743 ARG Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 899 GLU Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1257 LEU Chi-restraints excluded: chain o residue 1295 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 o residue 1479 LYS Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 298 MET Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 337 LYS Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 556 ILE Chi-restraints excluded: chain p residue 563 ASP Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 861 SER Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1069 ILE Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 110 LYS Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 2.9990 chunk 287 optimal weight: 0.2980 chunk 198 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 chunk 406 optimal weight: 0.0670 chunk 200 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 516 GLN ** o 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1163 HIS ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 312 GLN p 315 ASN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 718 GLN ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** 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** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 84 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36632 Z= 0.180 Angle : 0.443 9.471 49964 Z= 0.238 Chirality : 0.039 0.169 5568 Planarity : 0.003 0.040 6099 Dihedral : 16.336 144.494 5823 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.06 % Favored : 95.79 % Rotamer: Outliers : 4.07 % Allowed : 17.30 % Favored : 78.63 % 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: 0.95 (0.13), residues: 4137 helix: 2.07 (0.14), residues: 1399 sheet: 0.25 (0.20), residues: 665 loop : -0.19 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 679 HIS 0.016 0.001 HIS r 43 PHE 0.019 0.001 PHE o 234 TYR 0.014 0.001 TYR u 167 ARG 0.013 0.000 ARG p 975 *********************** 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 733 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 583 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.7004 (mmt90) cc_final: 0.6382 (mmt-90) REVERT: o 112 PHE cc_start: 0.7440 (t80) cc_final: 0.7145 (t80) REVERT: o 116 LYS cc_start: 0.7519 (mttt) cc_final: 0.6860 (mtmm) REVERT: o 136 GLN cc_start: 0.7595 (mt0) cc_final: 0.7092 (mp10) REVERT: o 138 LYS cc_start: 0.6368 (tttm) cc_final: 0.6164 (ttmm) REVERT: o 186 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6914 (mmm-85) REVERT: o 192 ARG cc_start: 0.7425 (ptm-80) cc_final: 0.7182 (ptm160) REVERT: o 197 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7578 (pt0) REVERT: o 201 GLU cc_start: 0.6218 (tt0) cc_final: 0.5838 (pt0) REVERT: o 219 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6849 (mp0) REVERT: o 227 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6602 (mtm-85) REVERT: o 233 CYS cc_start: 0.6243 (t) cc_final: 0.5851 (p) REVERT: o 238 MET cc_start: 0.7413 (mtt) cc_final: 0.6914 (mtp) REVERT: o 272 ASN cc_start: 0.7856 (m-40) cc_final: 0.7529 (t0) REVERT: o 382 ARG cc_start: 0.6349 (mtp-110) cc_final: 0.6074 (ttm110) REVERT: o 426 ARG cc_start: 0.7335 (mtm180) cc_final: 0.6877 (ptp-110) REVERT: o 486 LEU cc_start: 0.7386 (mt) cc_final: 0.7115 (mt) REVERT: o 514 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6332 (tt0) REVERT: o 524 MET cc_start: 0.8042 (mmp) cc_final: 0.7579 (mmm) REVERT: o 561 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7518 (mtm) REVERT: o 580 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7245 (mt) REVERT: o 612 ASP cc_start: 0.7130 (m-30) cc_final: 0.6739 (p0) REVERT: o 619 LYS cc_start: 0.6714 (mtpp) cc_final: 0.6447 (mttp) REVERT: o 634 GLU cc_start: 0.7132 (tt0) cc_final: 0.6530 (mt-10) REVERT: o 691 ASP cc_start: 0.7823 (m-30) cc_final: 0.7620 (m-30) REVERT: o 728 THR cc_start: 0.8003 (m) cc_final: 0.7479 (t) REVERT: o 803 LYS cc_start: 0.7488 (tttp) cc_final: 0.7155 (tptp) REVERT: o 818 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7272 (mp0) REVERT: o 861 GLN cc_start: 0.7266 (tp40) cc_final: 0.6582 (mt0) REVERT: o 876 ASP cc_start: 0.7348 (t0) cc_final: 0.6365 (t0) REVERT: o 899 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: o 900 SER cc_start: 0.8208 (m) cc_final: 0.7990 (t) REVERT: o 936 GLU cc_start: 0.7682 (tt0) cc_final: 0.7332 (tp30) REVERT: o 957 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6738 (mm-30) REVERT: o 1063 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7006 (mt-10) REVERT: o 1085 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6366 (tp30) REVERT: o 1104 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5213 (mm) REVERT: o 1132 LYS cc_start: 0.8117 (mptt) cc_final: 0.7742 (mppt) REVERT: o 1136 THR cc_start: 0.8305 (m) cc_final: 0.7998 (p) REVERT: o 1147 SER cc_start: 0.6963 (OUTLIER) cc_final: 0.6398 (t) REVERT: o 1262 MET cc_start: 0.7026 (ttt) cc_final: 0.6668 (tpp) REVERT: o 1286 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6767 (mtp85) REVERT: o 1306 LYS cc_start: 0.6175 (mttt) cc_final: 0.5664 (tttm) REVERT: o 1318 LYS cc_start: 0.5769 (mtpt) cc_final: 0.4982 (mtmp) REVERT: o 1337 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6258 (mt-10) REVERT: o 1361 ASP cc_start: 0.7514 (t0) cc_final: 0.7179 (t0) REVERT: o 1412 MET cc_start: 0.7217 (ttp) cc_final: 0.6740 (tmm) REVERT: o 1422 GLN cc_start: 0.6838 (mt0) cc_final: 0.5738 (mm-40) REVERT: o 1423 ASP cc_start: 0.8064 (m-30) cc_final: 0.7277 (t0) REVERT: o 1452 LYS cc_start: 0.7636 (mttt) cc_final: 0.6885 (mmtm) REVERT: p 49 GLU cc_start: 0.6424 (tp30) cc_final: 0.6010 (tp30) REVERT: p 53 MET cc_start: 0.6366 (mmm) cc_final: 0.5785 (mmm) REVERT: p 57 ARG cc_start: 0.5217 (ttp-110) cc_final: 0.4921 (mtm110) REVERT: p 168 ASP cc_start: 0.5717 (p0) cc_final: 0.5461 (m-30) REVERT: p 169 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6726 (ttp80) REVERT: p 222 ARG cc_start: 0.6185 (mtp-110) cc_final: 0.5901 (mtp85) REVERT: p 240 LEU cc_start: 0.7440 (mt) cc_final: 0.7204 (mm) REVERT: p 300 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8042 (mmm) REVERT: p 334 LYS cc_start: 0.7963 (tttt) cc_final: 0.7583 (tptt) REVERT: p 341 GLU cc_start: 0.7303 (tt0) cc_final: 0.6841 (tp30) REVERT: p 381 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7542 (mp0) REVERT: p 385 ARG cc_start: 0.6971 (ttm110) cc_final: 0.6027 (ttm-80) REVERT: p 386 ASP cc_start: 0.8006 (m-30) cc_final: 0.7307 (m-30) REVERT: p 463 ARG cc_start: 0.4745 (ttp-110) cc_final: 0.4183 (mtp180) REVERT: p 508 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.6558 (mtt) REVERT: p 551 GLU cc_start: 0.7658 (mp0) cc_final: 0.6904 (pm20) REVERT: p 597 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7457 (mm) REVERT: p 630 LYS cc_start: 0.7203 (mttt) cc_final: 0.6727 (mmtm) REVERT: p 683 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6840 (mm110) REVERT: p 728 MET cc_start: 0.7097 (mtm) cc_final: 0.6695 (mtp) REVERT: p 733 MET cc_start: 0.8091 (ttm) cc_final: 0.7734 (ttm) REVERT: p 745 ASP cc_start: 0.7435 (m-30) cc_final: 0.7160 (m-30) REVERT: p 771 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: p 796 MET cc_start: 0.8881 (mtm) cc_final: 0.8483 (mtm) REVERT: p 809 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7090 (p) REVERT: p 817 GLN cc_start: 0.7628 (tt0) cc_final: 0.6697 (pm20) REVERT: p 931 ILE cc_start: 0.7755 (pt) cc_final: 0.7396 (pp) REVERT: p 952 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: p 1041 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8025 (mp) REVERT: p 1054 MET cc_start: 0.8324 (mtm) cc_final: 0.7796 (mtm) REVERT: p 1080 ARG cc_start: 0.7305 (mtt90) cc_final: 0.6612 (mtp85) REVERT: p 1091 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.5099 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7641 (tp40) cc_final: 0.7054 (tt0) REVERT: p 1147 SER cc_start: 0.8311 (m) cc_final: 0.7645 (m) REVERT: p 1165 MET cc_start: 0.7986 (mtm) cc_final: 0.7601 (mtp) REVERT: p 1172 MET cc_start: 0.7418 (mmt) cc_final: 0.6729 (mmt) REVERT: q 17 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6880 (pm20) REVERT: q 81 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7006 (mttt) REVERT: q 106 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7400 (ttm-80) REVERT: q 126 ARG cc_start: 0.7689 (mtt180) cc_final: 0.6687 (mtp85) REVERT: q 158 GLU cc_start: 0.7296 (tt0) cc_final: 0.6499 (pt0) REVERT: q 199 LYS cc_start: 0.8109 (mttt) cc_final: 0.7547 (mtmm) REVERT: q 254 LYS cc_start: 0.6134 (tttt) cc_final: 0.5797 (mppt) REVERT: s 3 ASP cc_start: 0.5435 (m-30) cc_final: 0.4993 (t0) REVERT: s 95 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8771 (pp30) REVERT: s 108 GLN cc_start: 0.7827 (mt0) cc_final: 0.7471 (tt0) REVERT: s 126 ILE cc_start: 0.7600 (mt) cc_final: 0.7314 (mp) REVERT: s 158 GLU cc_start: 0.6236 (tt0) cc_final: 0.5964 (pt0) REVERT: s 167 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6711 (mp0) REVERT: t 57 MET cc_start: 0.7868 (ttp) cc_final: 0.7449 (ttm) REVERT: t 59 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.6181 (ptmt) REVERT: t 86 GLU cc_start: 0.6158 (mm-30) cc_final: 0.5791 (mm-30) REVERT: t 95 LYS cc_start: 0.6194 (ttmm) cc_final: 0.5976 (mtpp) REVERT: t 116 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7525 (mt-10) REVERT: u 12 LEU cc_start: 0.8457 (mp) cc_final: 0.8255 (mm) REVERT: u 68 TYR cc_start: 0.6101 (m-80) cc_final: 0.5881 (m-80) REVERT: u 101 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6967 (pp) REVERT: u 104 MET cc_start: 0.7613 (ttp) cc_final: 0.7176 (tmm) REVERT: v 20 LYS cc_start: 0.7408 (tttt) cc_final: 0.7138 (mmmm) REVERT: v 28 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6280 (mt) REVERT: v 37 MET cc_start: 0.7657 (mtp) cc_final: 0.7398 (mtp) REVERT: v 51 ASP cc_start: 0.7667 (m-30) cc_final: 0.7004 (p0) REVERT: v 63 THR cc_start: 0.8467 (p) cc_final: 0.8103 (t) REVERT: v 100 GLU cc_start: 0.6715 (tt0) cc_final: 0.5973 (mt-10) REVERT: v 126 GLN cc_start: 0.7298 (tt0) cc_final: 0.6955 (tt0) REVERT: v 136 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6843 (pt0) REVERT: v 146 LYS cc_start: 0.6715 (tttt) cc_final: 0.6240 (tttm) REVERT: w 71 ASP cc_start: 0.7625 (m-30) cc_final: 0.7387 (m-30) REVERT: x 19 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: x 41 LYS cc_start: 0.8109 (mptt) cc_final: 0.7838 (mmtp) REVERT: y 8 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6861 (mt-10) REVERT: y 14 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7874 (mp0) REVERT: y 16 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6255 (tt0) REVERT: y 17 LYS cc_start: 0.7291 (mtpp) cc_final: 0.6929 (mmmm) REVERT: y 23 LYS cc_start: 0.8195 (mttt) cc_final: 0.7930 (ttpp) REVERT: y 35 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7192 (mm) REVERT: y 47 LYS cc_start: 0.6670 (ttpp) cc_final: 0.6304 (tttm) REVERT: y 48 SER cc_start: 0.7975 (t) cc_final: 0.7709 (p) REVERT: y 84 GLN cc_start: 0.6817 (mp10) cc_final: 0.6399 (mp-120) REVERT: y 85 GLU cc_start: 0.6334 (mt-10) cc_final: 0.5710 (tt0) REVERT: z 15 MET cc_start: 0.6393 (mmm) cc_final: 0.6018 (mmt) REVERT: z 16 ILE cc_start: 0.8279 (mt) cc_final: 0.7784 (mp) REVERT: z 25 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6994 (pm20) REVERT: z 27 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6735 (tp30) REVERT: z 38 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8248 (pt0) outliers start: 150 outliers final: 58 residues processed: 671 average time/residue: 1.6953 time to fit residues: 1352.4570 Evaluate side-chains 642 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 561 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 186 ARG Chi-restraints excluded: chain o residue 227 ARG Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 899 GLU Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1139 LEU Chi-restraints excluded: chain o residue 1140 THR 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 1295 ASP Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain p residue 20 ASP Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 337 LYS Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 529 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 861 SER Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain t residue 59 LYS Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 156 ASP Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 107 GLU Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 0.7980 chunk 231 optimal weight: 0.8980 chunk 5 optimal weight: 40.0000 chunk 302 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 347 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 365 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 204 HIS ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 765 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1101 GLN ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 56 GLN ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 254 GLN p 265 GLN p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 133 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN y 29 ASN z 23 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36632 Z= 0.246 Angle : 0.474 10.605 49964 Z= 0.252 Chirality : 0.040 0.172 5568 Planarity : 0.003 0.040 6099 Dihedral : 16.240 140.861 5823 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 4.50 % Allowed : 17.79 % Favored : 77.71 % 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: 2.01 (0.14), residues: 1403 sheet: 0.10 (0.19), residues: 699 loop : -0.19 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 479 HIS 0.015 0.001 HIS r 43 PHE 0.020 0.001 PHE o 234 TYR 0.020 0.001 TYR q 231 ARG 0.010 0.000 ARG p 975 *********************** 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 732 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 566 time to evaluate : 4.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.6913 (mmt90) cc_final: 0.6295 (mmt-90) REVERT: o 116 LYS cc_start: 0.7518 (mttt) cc_final: 0.6842 (mtmm) REVERT: o 120 ASP cc_start: 0.7670 (m-30) cc_final: 0.7397 (m-30) REVERT: o 136 GLN cc_start: 0.7592 (mt0) cc_final: 0.7123 (mp10) REVERT: o 138 LYS cc_start: 0.6493 (tttm) cc_final: 0.6181 (ttmm) REVERT: o 186 ARG cc_start: 0.6994 (mmm-85) cc_final: 0.6752 (mmm-85) REVERT: o 197 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7621 (pt0) REVERT: o 201 GLU cc_start: 0.6202 (tt0) cc_final: 0.5845 (pt0) REVERT: o 219 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6830 (mp0) REVERT: o 227 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6594 (mtm-85) REVERT: o 233 CYS cc_start: 0.6128 (t) cc_final: 0.5816 (p) REVERT: o 238 MET cc_start: 0.7390 (mtt) cc_final: 0.6888 (mtp) REVERT: o 272 ASN cc_start: 0.7938 (m-40) cc_final: 0.7571 (t0) REVERT: o 305 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6996 (mm-30) REVERT: o 382 ARG cc_start: 0.6511 (mtp-110) cc_final: 0.6202 (ttm110) REVERT: o 426 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7069 (ptp-110) REVERT: o 473 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6406 (mtm-85) REVERT: o 514 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6318 (tt0) REVERT: o 524 MET cc_start: 0.8001 (mmp) cc_final: 0.7547 (mmm) REVERT: o 561 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7476 (mtm) REVERT: o 580 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7265 (mt) REVERT: o 612 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6766 (p0) REVERT: o 619 LYS cc_start: 0.6716 (mtpp) cc_final: 0.6416 (mttp) REVERT: o 634 GLU cc_start: 0.7232 (tt0) cc_final: 0.6615 (mt-10) REVERT: o 726 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: o 728 THR cc_start: 0.8039 (m) cc_final: 0.7504 (t) REVERT: o 775 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7622 (ttmm) REVERT: o 803 LYS cc_start: 0.7505 (tttp) cc_final: 0.7083 (tptt) REVERT: o 818 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7250 (mp0) REVERT: o 861 GLN cc_start: 0.7238 (tp40) cc_final: 0.6572 (mt0) REVERT: o 876 ASP cc_start: 0.7360 (t0) cc_final: 0.6323 (t0) REVERT: o 900 SER cc_start: 0.8177 (m) cc_final: 0.7958 (t) REVERT: o 936 GLU cc_start: 0.7712 (tt0) cc_final: 0.7354 (tp30) REVERT: o 1063 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6997 (mt-10) REVERT: o 1085 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6279 (tp30) REVERT: o 1104 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5249 (mm) REVERT: o 1132 LYS cc_start: 0.8145 (mptt) cc_final: 0.7688 (mppt) REVERT: o 1136 THR cc_start: 0.8294 (m) cc_final: 0.7944 (p) REVERT: o 1147 SER cc_start: 0.6969 (OUTLIER) cc_final: 0.6473 (t) REVERT: o 1262 MET cc_start: 0.7023 (ttt) cc_final: 0.6724 (tpp) REVERT: o 1286 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6796 (mtp85) REVERT: o 1306 LYS cc_start: 0.6170 (mttt) cc_final: 0.5678 (tttm) REVERT: o 1309 MET cc_start: 0.8597 (ptm) cc_final: 0.7837 (ttp) REVERT: o 1318 LYS cc_start: 0.5787 (mtpt) cc_final: 0.5018 (mtmp) REVERT: o 1324 GLU cc_start: 0.6696 (mp0) cc_final: 0.6236 (tp30) REVERT: o 1337 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6276 (mt-10) REVERT: o 1361 ASP cc_start: 0.7709 (t0) cc_final: 0.7331 (t0) REVERT: o 1412 MET cc_start: 0.7319 (ttp) cc_final: 0.6870 (tmm) REVERT: o 1422 GLN cc_start: 0.6852 (mt0) cc_final: 0.5762 (mm-40) REVERT: o 1423 ASP cc_start: 0.8108 (m-30) cc_final: 0.7256 (t0) REVERT: o 1452 LYS cc_start: 0.7538 (mttt) cc_final: 0.6782 (mmtm) REVERT: o 1460 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6980 (mp) REVERT: p 49 GLU cc_start: 0.6429 (tp30) cc_final: 0.5951 (tp30) REVERT: p 53 MET cc_start: 0.6438 (mmm) cc_final: 0.5889 (mmm) REVERT: p 57 ARG cc_start: 0.5279 (ttp-110) cc_final: 0.4941 (mtm110) REVERT: p 168 ASP cc_start: 0.5746 (p0) cc_final: 0.5477 (m-30) REVERT: p 169 ARG cc_start: 0.7153 (ttt-90) cc_final: 0.6729 (ttp80) REVERT: p 222 ARG cc_start: 0.6227 (mtp-110) cc_final: 0.5855 (mtt-85) REVERT: p 240 LEU cc_start: 0.7562 (mt) cc_final: 0.7228 (mm) REVERT: p 334 LYS cc_start: 0.7979 (tttt) cc_final: 0.7594 (tptt) REVERT: p 335 ARG cc_start: 0.6574 (mtm180) cc_final: 0.6132 (mtm-85) REVERT: p 345 LYS cc_start: 0.6595 (mptt) cc_final: 0.6395 (mmtm) REVERT: p 358 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6518 (pm20) REVERT: p 381 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7525 (mp0) REVERT: p 385 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6073 (ttm-80) REVERT: p 386 ASP cc_start: 0.8012 (m-30) cc_final: 0.7301 (m-30) REVERT: p 508 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.5905 (mtt) REVERT: p 551 GLU cc_start: 0.7527 (mp0) cc_final: 0.6764 (pm20) REVERT: p 597 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7523 (mm) REVERT: p 606 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6516 (t0) REVERT: p 630 LYS cc_start: 0.7121 (mttt) cc_final: 0.6720 (mmtm) REVERT: p 636 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6469 (mmmt) REVERT: p 728 MET cc_start: 0.7163 (mtm) cc_final: 0.6791 (mtp) REVERT: p 733 MET cc_start: 0.8143 (ttm) cc_final: 0.7803 (ttm) REVERT: p 745 ASP cc_start: 0.7317 (m-30) cc_final: 0.7099 (m-30) REVERT: p 761 THR cc_start: 0.7800 (m) cc_final: 0.7443 (p) REVERT: p 771 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: p 796 MET cc_start: 0.8912 (mtm) cc_final: 0.8547 (mtm) REVERT: p 809 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7054 (p) REVERT: p 817 GLN cc_start: 0.7681 (tt0) cc_final: 0.6722 (pm20) REVERT: p 931 ILE cc_start: 0.7789 (pt) cc_final: 0.7390 (pp) REVERT: p 952 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: p 1054 MET cc_start: 0.8364 (mtm) cc_final: 0.7872 (mtm) REVERT: p 1080 ARG cc_start: 0.7281 (mtt90) cc_final: 0.6522 (mtp85) REVERT: p 1091 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.5107 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7610 (tp40) cc_final: 0.7086 (tt0) REVERT: p 1147 SER cc_start: 0.8449 (m) cc_final: 0.8015 (m) REVERT: p 1165 MET cc_start: 0.7974 (mtm) cc_final: 0.7609 (mtp) REVERT: p 1172 MET cc_start: 0.7414 (mmt) cc_final: 0.6693 (mmt) REVERT: q 17 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6823 (pm20) REVERT: q 20 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7164 (mtmt) REVERT: q 81 LYS cc_start: 0.7582 (mtpt) cc_final: 0.7075 (mttt) REVERT: q 96 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6879 (mp0) REVERT: q 126 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6680 (mtp85) REVERT: q 155 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6281 (tppp) REVERT: q 158 GLU cc_start: 0.7244 (tt0) cc_final: 0.6449 (pt0) REVERT: q 199 LYS cc_start: 0.8165 (mttt) cc_final: 0.7559 (mtmm) REVERT: q 254 LYS cc_start: 0.6175 (tttt) cc_final: 0.5815 (mppt) REVERT: s 3 ASP cc_start: 0.5489 (m-30) cc_final: 0.5038 (t0) REVERT: s 98 ASN cc_start: 0.9030 (t0) cc_final: 0.8784 (t0) REVERT: s 104 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6382 (mm) REVERT: s 108 GLN cc_start: 0.7796 (mt0) cc_final: 0.7512 (tt0) REVERT: s 126 ILE cc_start: 0.7411 (mt) cc_final: 0.7118 (mp) REVERT: s 158 GLU cc_start: 0.6238 (tt0) cc_final: 0.6006 (pt0) REVERT: t 57 MET cc_start: 0.7874 (ttp) cc_final: 0.7507 (ttm) REVERT: t 59 LYS cc_start: 0.6435 (OUTLIER) cc_final: 0.6103 (ptmt) REVERT: t 86 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5885 (mm-30) REVERT: u 16 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6427 (ptp-170) REVERT: u 24 ASN cc_start: 0.6195 (t0) cc_final: 0.5632 (t0) REVERT: u 101 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.6998 (pp) REVERT: u 104 MET cc_start: 0.7341 (ttp) cc_final: 0.6814 (tmm) REVERT: v 20 LYS cc_start: 0.7420 (tttt) cc_final: 0.7046 (tptp) REVERT: v 28 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6235 (mt) REVERT: v 36 LYS cc_start: 0.6347 (mmtm) cc_final: 0.5757 (mmpt) REVERT: v 51 ASP cc_start: 0.7672 (m-30) cc_final: 0.6950 (p0) REVERT: v 63 THR cc_start: 0.8468 (p) cc_final: 0.8095 (t) REVERT: v 100 GLU cc_start: 0.6705 (tt0) cc_final: 0.5996 (mt-10) REVERT: v 126 GLN cc_start: 0.7292 (tt0) cc_final: 0.6965 (tt0) REVERT: v 136 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6867 (pt0) REVERT: v 146 LYS cc_start: 0.6726 (tttt) cc_final: 0.6230 (tttm) REVERT: w 71 ASP cc_start: 0.7699 (m-30) cc_final: 0.7391 (m-30) REVERT: x 19 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: x 66 GLU cc_start: 0.6453 (tt0) cc_final: 0.5746 (pm20) REVERT: y 8 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6840 (mt-10) REVERT: y 14 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7863 (mp0) REVERT: y 16 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6286 (tt0) REVERT: y 17 LYS cc_start: 0.7339 (mtpp) cc_final: 0.7073 (mmmm) REVERT: y 23 LYS cc_start: 0.8221 (mttt) cc_final: 0.7816 (ttpp) REVERT: y 29 ASN cc_start: 0.6821 (OUTLIER) cc_final: 0.6486 (m110) REVERT: y 35 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7152 (mm) REVERT: y 47 LYS cc_start: 0.6690 (ttpp) cc_final: 0.6347 (tttm) REVERT: y 48 SER cc_start: 0.7991 (t) cc_final: 0.7715 (p) REVERT: y 84 GLN cc_start: 0.6847 (mp10) cc_final: 0.6423 (mp-120) REVERT: y 85 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5706 (tt0) REVERT: y 103 GLU cc_start: 0.7046 (tp30) cc_final: 0.6816 (tp30) REVERT: z 15 MET cc_start: 0.6399 (mmm) cc_final: 0.6012 (mmt) REVERT: z 16 ILE cc_start: 0.8313 (mt) cc_final: 0.7834 (mp) REVERT: z 25 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: z 27 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6811 (tp30) REVERT: z 38 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7904 (pm20) outliers start: 166 outliers final: 89 residues processed: 669 average time/residue: 1.6195 time to fit residues: 1285.4285 Evaluate side-chains 674 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 553 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 191 ILE Chi-restraints excluded: chain o residue 227 ARG Chi-restraints excluded: chain o residue 229 SER Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 726 GLU Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1140 THR 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 1257 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1460 LEU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 20 ASP Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 385 ARG Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 636 LYS Chi-restraints excluded: chain p residue 672 THR Chi-restraints excluded: chain p residue 673 VAL Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1118 VAL Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 20 LYS Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 117 SER Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 59 LYS Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 4 HIS Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 11 ASP Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 29 ASN Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU 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: 0.0000 chunk 80 optimal weight: 0.8980 chunk 238 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 407 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1024 ASN o1101 GLN o1163 HIS ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS o1445 HIS ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36632 Z= 0.167 Angle : 0.430 9.998 49964 Z= 0.230 Chirality : 0.039 0.168 5568 Planarity : 0.003 0.038 6099 Dihedral : 16.129 137.905 5823 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.50 % Favored : 95.33 % Rotamer: Outliers : 3.99 % Allowed : 18.44 % Favored : 77.58 % 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: 1.01 (0.13), residues: 4137 helix: 2.17 (0.14), residues: 1407 sheet: 0.20 (0.19), residues: 693 loop : -0.18 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 679 HIS 0.016 0.001 HIS r 43 PHE 0.011 0.001 PHE s 44 TYR 0.015 0.001 TYR t 115 ARG 0.008 0.000 ARG p 463 *********************** 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 714 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 567 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.6905 (mmt90) cc_final: 0.6260 (mmt-90) REVERT: o 116 LYS cc_start: 0.7535 (mttt) cc_final: 0.6885 (mtmm) REVERT: o 120 ASP cc_start: 0.7663 (m-30) cc_final: 0.7388 (m-30) REVERT: o 136 GLN cc_start: 0.7582 (mt0) cc_final: 0.7117 (mp10) REVERT: o 138 LYS cc_start: 0.6479 (tttm) cc_final: 0.6242 (mttp) REVERT: o 186 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6762 (mmm-85) REVERT: o 192 ARG cc_start: 0.7465 (ptm160) cc_final: 0.7052 (ptm160) REVERT: o 197 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7595 (pt0) REVERT: o 201 GLU cc_start: 0.6224 (tt0) cc_final: 0.5822 (pt0) REVERT: o 219 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6817 (mp0) REVERT: o 233 CYS cc_start: 0.6153 (t) cc_final: 0.5835 (p) REVERT: o 238 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6709 (mtp) REVERT: o 272 ASN cc_start: 0.7848 (m-40) cc_final: 0.7551 (t0) REVERT: o 305 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6980 (mm-30) REVERT: o 382 ARG cc_start: 0.6516 (mtp-110) cc_final: 0.6210 (ttm110) REVERT: o 426 ARG cc_start: 0.7752 (mtm180) cc_final: 0.7217 (ptp-110) REVERT: o 473 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6423 (mtm-85) REVERT: o 486 LEU cc_start: 0.7267 (mt) cc_final: 0.7017 (mt) REVERT: o 514 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6318 (tt0) REVERT: o 524 MET cc_start: 0.8012 (mmp) cc_final: 0.7564 (mmm) REVERT: o 561 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7266 (mtm) REVERT: o 580 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7254 (mt) REVERT: o 612 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6803 (p0) REVERT: o 619 LYS cc_start: 0.6683 (mtpp) cc_final: 0.6403 (mttp) REVERT: o 634 GLU cc_start: 0.7316 (tt0) cc_final: 0.6664 (mt-10) REVERT: o 637 MET cc_start: 0.7712 (ptm) cc_final: 0.7491 (ptt) REVERT: o 728 THR cc_start: 0.8043 (m) cc_final: 0.7488 (t) REVERT: o 775 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7687 (ttmm) REVERT: o 803 LYS cc_start: 0.7502 (tttp) cc_final: 0.7081 (tptt) REVERT: o 818 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7217 (mp0) REVERT: o 861 GLN cc_start: 0.7373 (tp40) cc_final: 0.6715 (mt0) REVERT: o 867 SER cc_start: 0.7010 (OUTLIER) cc_final: 0.6767 (m) REVERT: o 876 ASP cc_start: 0.7368 (t0) cc_final: 0.6339 (t0) REVERT: o 900 SER cc_start: 0.8172 (m) cc_final: 0.7954 (t) REVERT: o 936 GLU cc_start: 0.7663 (tt0) cc_final: 0.7337 (tp30) REVERT: o 1063 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7036 (mt-10) REVERT: o 1085 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6273 (tp30) REVERT: o 1132 LYS cc_start: 0.8118 (mptt) cc_final: 0.7672 (mppt) REVERT: o 1136 THR cc_start: 0.8317 (m) cc_final: 0.8000 (p) REVERT: o 1147 SER cc_start: 0.6862 (OUTLIER) cc_final: 0.6375 (t) REVERT: o 1262 MET cc_start: 0.7015 (ttt) cc_final: 0.6788 (tpp) REVERT: o 1286 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.6819 (mtp85) REVERT: o 1306 LYS cc_start: 0.6186 (mttt) cc_final: 0.5692 (tttm) REVERT: o 1309 MET cc_start: 0.8577 (ptm) cc_final: 0.7867 (ttp) REVERT: o 1324 GLU cc_start: 0.6701 (mp0) cc_final: 0.6247 (tp30) REVERT: o 1337 GLU cc_start: 0.6433 (mt-10) cc_final: 0.6184 (mt-10) REVERT: o 1361 ASP cc_start: 0.7740 (t0) cc_final: 0.7350 (t0) REVERT: o 1412 MET cc_start: 0.7308 (ttp) cc_final: 0.6853 (tmm) REVERT: o 1422 GLN cc_start: 0.6855 (mt0) cc_final: 0.5754 (mm-40) REVERT: o 1423 ASP cc_start: 0.8096 (m-30) cc_final: 0.7418 (t0) REVERT: o 1452 LYS cc_start: 0.7508 (mttt) cc_final: 0.6845 (mmtt) REVERT: o 1460 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6942 (mp) REVERT: p 49 GLU cc_start: 0.6368 (tp30) cc_final: 0.5974 (tp30) REVERT: p 53 MET cc_start: 0.6431 (mmm) cc_final: 0.5865 (mmm) REVERT: p 57 ARG cc_start: 0.5283 (ttp-110) cc_final: 0.4945 (mtm110) REVERT: p 168 ASP cc_start: 0.5732 (p0) cc_final: 0.5481 (m-30) REVERT: p 169 ARG cc_start: 0.7140 (ttt-90) cc_final: 0.6722 (ttp80) REVERT: p 222 ARG cc_start: 0.6139 (mtp-110) cc_final: 0.5848 (mtp85) REVERT: p 300 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8027 (mmm) REVERT: p 324 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.5947 (mmm-85) REVERT: p 334 LYS cc_start: 0.7980 (tttt) cc_final: 0.7596 (tptt) REVERT: p 335 ARG cc_start: 0.6542 (mtm180) cc_final: 0.6130 (mtm-85) REVERT: p 336 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6451 (mt) REVERT: p 358 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6547 (pm20) REVERT: p 381 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7510 (mp0) REVERT: p 385 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6076 (ttm-80) REVERT: p 386 ASP cc_start: 0.8080 (m-30) cc_final: 0.7314 (m-30) REVERT: p 463 ARG cc_start: 0.4410 (ttp-110) cc_final: 0.3882 (mtp180) REVERT: p 508 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6534 (mtt) REVERT: p 550 MET cc_start: 0.5749 (ttp) cc_final: 0.5100 (tmm) REVERT: p 551 GLU cc_start: 0.7503 (mp0) cc_final: 0.6732 (pm20) REVERT: p 630 LYS cc_start: 0.7097 (mttt) cc_final: 0.6677 (mmtm) REVERT: p 636 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6466 (mmmt) REVERT: p 728 MET cc_start: 0.7156 (mtm) cc_final: 0.6770 (mtp) REVERT: p 733 MET cc_start: 0.8150 (ttm) cc_final: 0.7828 (ttm) REVERT: p 745 ASP cc_start: 0.6771 (m-30) cc_final: 0.6569 (m-30) REVERT: p 761 THR cc_start: 0.7780 (m) cc_final: 0.7427 (p) REVERT: p 771 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: p 796 MET cc_start: 0.8897 (mtm) cc_final: 0.8543 (mtm) REVERT: p 809 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7082 (p) REVERT: p 817 GLN cc_start: 0.7652 (tt0) cc_final: 0.6658 (pm20) REVERT: p 931 ILE cc_start: 0.7729 (pt) cc_final: 0.7354 (pp) REVERT: p 952 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: p 1041 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8062 (mp) REVERT: p 1054 MET cc_start: 0.8291 (mtm) cc_final: 0.7803 (mtm) REVERT: p 1080 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6550 (mtp85) REVERT: p 1091 ARG cc_start: 0.5527 (OUTLIER) cc_final: 0.5079 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7748 (tp40) cc_final: 0.7180 (tt0) REVERT: p 1147 SER cc_start: 0.8295 (m) cc_final: 0.7931 (m) REVERT: p 1165 MET cc_start: 0.7986 (mtm) cc_final: 0.7632 (mtp) REVERT: p 1172 MET cc_start: 0.7634 (mmt) cc_final: 0.7196 (mmt) REVERT: q 17 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6842 (pm20) REVERT: q 41 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: q 81 LYS cc_start: 0.7557 (mtpt) cc_final: 0.7002 (mttt) REVERT: q 94 CYS cc_start: 0.5395 (OUTLIER) cc_final: 0.5192 (p) REVERT: q 96 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6978 (mp0) REVERT: q 126 ARG cc_start: 0.7783 (mtt180) cc_final: 0.6820 (mtp180) REVERT: q 155 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6260 (tppp) REVERT: q 158 GLU cc_start: 0.7166 (tt0) cc_final: 0.6448 (pt0) REVERT: q 199 LYS cc_start: 0.8140 (mttt) cc_final: 0.7518 (mtmm) REVERT: q 254 LYS cc_start: 0.6120 (tttt) cc_final: 0.5778 (mppt) REVERT: s 3 ASP cc_start: 0.5460 (m-30) cc_final: 0.5157 (m-30) REVERT: s 95 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8780 (pp30) REVERT: s 98 ASN cc_start: 0.9002 (t0) cc_final: 0.8780 (t0) REVERT: s 104 ILE cc_start: 0.6673 (OUTLIER) cc_final: 0.6384 (mm) REVERT: s 108 GLN cc_start: 0.7822 (mt0) cc_final: 0.7534 (tt0) REVERT: s 126 ILE cc_start: 0.7360 (mt) cc_final: 0.7090 (mp) REVERT: s 158 GLU cc_start: 0.6223 (tt0) cc_final: 0.5988 (pt0) REVERT: t 57 MET cc_start: 0.7867 (ttp) cc_final: 0.7454 (ttm) REVERT: t 59 LYS cc_start: 0.6417 (OUTLIER) cc_final: 0.6083 (ptmt) REVERT: t 116 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7534 (mt-10) REVERT: u 101 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7052 (pp) REVERT: u 104 MET cc_start: 0.7391 (ttp) cc_final: 0.6822 (tmm) REVERT: v 20 LYS cc_start: 0.7440 (tttt) cc_final: 0.7049 (tptp) REVERT: v 28 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6550 (mt) REVERT: v 51 ASP cc_start: 0.7728 (m-30) cc_final: 0.6955 (p0) REVERT: v 54 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: v 57 ARG cc_start: 0.7274 (ttp80) cc_final: 0.6908 (ttp80) REVERT: v 63 THR cc_start: 0.8457 (p) cc_final: 0.8096 (t) REVERT: v 100 GLU cc_start: 0.6697 (tt0) cc_final: 0.5994 (mt-10) REVERT: v 126 GLN cc_start: 0.7225 (tt0) cc_final: 0.6979 (tt0) REVERT: v 133 HIS cc_start: 0.7282 (m170) cc_final: 0.6881 (m-70) REVERT: v 136 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6775 (pt0) REVERT: v 146 LYS cc_start: 0.6720 (tttt) cc_final: 0.6210 (tttm) REVERT: w 27 LYS cc_start: 0.6889 (pttm) cc_final: 0.6426 (pptt) REVERT: w 71 ASP cc_start: 0.7662 (m-30) cc_final: 0.7374 (m-30) REVERT: x 19 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: x 41 LYS cc_start: 0.8156 (mptt) cc_final: 0.7856 (mmtm) REVERT: x 66 GLU cc_start: 0.6434 (tt0) cc_final: 0.5732 (pm20) REVERT: y 8 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6814 (mt-10) REVERT: y 14 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7897 (mp0) REVERT: y 16 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6286 (tt0) REVERT: y 17 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7118 (mmmm) REVERT: y 23 LYS cc_start: 0.8172 (mttt) cc_final: 0.7797 (ttpp) REVERT: y 35 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7128 (mm) REVERT: y 47 LYS cc_start: 0.6659 (ttpp) cc_final: 0.6297 (tttm) REVERT: y 48 SER cc_start: 0.7967 (t) cc_final: 0.7702 (p) REVERT: y 84 GLN cc_start: 0.6821 (mp10) cc_final: 0.6414 (mp-120) REVERT: y 85 GLU cc_start: 0.6306 (mt-10) cc_final: 0.5671 (tt0) REVERT: y 103 GLU cc_start: 0.7047 (tp30) cc_final: 0.6473 (tp30) REVERT: z 15 MET cc_start: 0.6353 (mmm) cc_final: 0.5953 (mmt) REVERT: z 16 ILE cc_start: 0.8333 (mt) cc_final: 0.7857 (mp) REVERT: z 25 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: z 27 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6826 (tp30) REVERT: z 38 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7906 (pm20) outliers start: 147 outliers final: 77 residues processed: 654 average time/residue: 1.6104 time to fit residues: 1254.3824 Evaluate side-chains 668 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 557 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 186 ARG Chi-restraints excluded: chain o residue 229 SER Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 517 GLU Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 867 SER Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1257 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1460 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 324 ARG Chi-restraints excluded: chain p residue 336 ILE Chi-restraints excluded: chain p residue 385 ARG Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 636 LYS Chi-restraints excluded: chain p residue 638 ARG Chi-restraints excluded: chain p residue 673 VAL Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 59 LYS Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 11 ASP Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 232 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 342 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 405 optimal weight: 2.9990 chunk 253 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 22 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1101 GLN o1163 HIS ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 718 GLN ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN z 23 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36632 Z= 0.201 Angle : 0.445 10.255 49964 Z= 0.236 Chirality : 0.039 0.169 5568 Planarity : 0.003 0.038 6099 Dihedral : 15.991 133.182 5823 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.57 % Favored : 95.26 % Rotamer: Outliers : 4.34 % Allowed : 18.22 % Favored : 77.44 % 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: 1.00 (0.13), residues: 4137 helix: 2.14 (0.14), residues: 1414 sheet: 0.15 (0.19), residues: 693 loop : -0.16 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 479 HIS 0.013 0.001 HIS r 43 PHE 0.020 0.001 PHE o 234 TYR 0.017 0.001 TYR t 115 ARG 0.006 0.000 ARG p 463 *********************** 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 722 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 562 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.6893 (mmt90) cc_final: 0.6177 (mmt-90) REVERT: o 19 LYS cc_start: 0.7216 (mmtp) cc_final: 0.7006 (tppp) REVERT: o 116 LYS cc_start: 0.7540 (mttt) cc_final: 0.6876 (mtmm) REVERT: o 120 ASP cc_start: 0.7683 (m-30) cc_final: 0.7433 (m-30) REVERT: o 136 GLN cc_start: 0.7583 (mt0) cc_final: 0.7095 (mp10) REVERT: o 192 ARG cc_start: 0.7444 (ptm160) cc_final: 0.6920 (ptt90) REVERT: o 197 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7548 (pt0) REVERT: o 219 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6791 (mp0) REVERT: o 233 CYS cc_start: 0.6235 (t) cc_final: 0.5846 (p) REVERT: o 238 MET cc_start: 0.7271 (mtt) cc_final: 0.6790 (mtp) REVERT: o 271 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7404 (mmm-85) REVERT: o 272 ASN cc_start: 0.7820 (m-40) cc_final: 0.7475 (t0) REVERT: o 305 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7004 (mm-30) REVERT: o 306 ASP cc_start: 0.7627 (m-30) cc_final: 0.7265 (m-30) REVERT: o 382 ARG cc_start: 0.6328 (mtp-110) cc_final: 0.6030 (ttm110) REVERT: o 426 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7232 (ptp-110) REVERT: o 473 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6388 (mtm-85) REVERT: o 486 LEU cc_start: 0.7297 (mt) cc_final: 0.7045 (mt) REVERT: o 514 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6383 (tt0) REVERT: o 524 MET cc_start: 0.7998 (mmp) cc_final: 0.7541 (mmm) REVERT: o 561 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7368 (mtm) REVERT: o 580 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7269 (mt) REVERT: o 612 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6861 (p0) REVERT: o 619 LYS cc_start: 0.6910 (mtpp) cc_final: 0.6635 (mttp) REVERT: o 634 GLU cc_start: 0.7295 (tt0) cc_final: 0.6588 (mt-10) REVERT: o 728 THR cc_start: 0.7986 (m) cc_final: 0.7441 (t) REVERT: o 775 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7816 (ttmm) REVERT: o 803 LYS cc_start: 0.7515 (tttp) cc_final: 0.7122 (tptp) REVERT: o 818 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7475 (mt-10) REVERT: o 861 GLN cc_start: 0.7272 (tp40) cc_final: 0.6648 (mt0) REVERT: o 867 SER cc_start: 0.6934 (OUTLIER) cc_final: 0.6687 (m) REVERT: o 876 ASP cc_start: 0.7405 (t0) cc_final: 0.6368 (t0) REVERT: o 900 SER cc_start: 0.8154 (m) cc_final: 0.7923 (t) REVERT: o 936 GLU cc_start: 0.7696 (tt0) cc_final: 0.7434 (tp30) REVERT: o 1026 ASP cc_start: 0.7851 (p0) cc_final: 0.7569 (p0) REVERT: o 1063 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7058 (mt-10) REVERT: o 1085 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6276 (tp30) REVERT: o 1132 LYS cc_start: 0.8061 (mptt) cc_final: 0.7632 (mppt) REVERT: o 1136 THR cc_start: 0.8296 (m) cc_final: 0.7931 (p) REVERT: o 1147 SER cc_start: 0.6803 (OUTLIER) cc_final: 0.6303 (t) REVERT: o 1162 GLU cc_start: 0.7235 (tt0) cc_final: 0.7010 (tt0) REVERT: o 1228 MET cc_start: 0.7810 (tpp) cc_final: 0.7563 (mmt) REVERT: o 1286 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.6958 (mtp85) REVERT: o 1306 LYS cc_start: 0.6151 (mttt) cc_final: 0.5689 (tttm) REVERT: o 1309 MET cc_start: 0.8573 (ptm) cc_final: 0.7822 (ttp) REVERT: o 1324 GLU cc_start: 0.6617 (mp0) cc_final: 0.6215 (tp30) REVERT: o 1337 GLU cc_start: 0.6240 (mt-10) cc_final: 0.6022 (mt-10) REVERT: o 1361 ASP cc_start: 0.7821 (t0) cc_final: 0.7440 (t0) REVERT: o 1412 MET cc_start: 0.7362 (ttp) cc_final: 0.6791 (tmm) REVERT: o 1422 GLN cc_start: 0.6794 (mt0) cc_final: 0.5727 (mm-40) REVERT: o 1423 ASP cc_start: 0.8036 (m-30) cc_final: 0.7185 (t0) REVERT: o 1452 LYS cc_start: 0.7409 (mttt) cc_final: 0.6761 (mptt) REVERT: o 1460 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6944 (mp) REVERT: p 49 GLU cc_start: 0.6362 (tp30) cc_final: 0.5848 (tp30) REVERT: p 53 MET cc_start: 0.6444 (mmm) cc_final: 0.5890 (mmm) REVERT: p 57 ARG cc_start: 0.5336 (ttp-110) cc_final: 0.4983 (mtm110) REVERT: p 168 ASP cc_start: 0.5677 (p0) cc_final: 0.5399 (m-30) REVERT: p 169 ARG cc_start: 0.7137 (ttt-90) cc_final: 0.6721 (ttp80) REVERT: p 222 ARG cc_start: 0.6213 (mtp-110) cc_final: 0.5836 (mtp85) REVERT: p 300 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8057 (mmm) REVERT: p 324 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.5897 (mmm-85) REVERT: p 334 LYS cc_start: 0.8001 (tttt) cc_final: 0.7585 (tptt) REVERT: p 335 ARG cc_start: 0.6338 (mtm180) cc_final: 0.5930 (mtm-85) REVERT: p 336 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6427 (mt) REVERT: p 358 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6701 (pm20) REVERT: p 381 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7523 (mp0) REVERT: p 385 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6101 (ttm-80) REVERT: p 386 ASP cc_start: 0.7852 (m-30) cc_final: 0.7113 (m-30) REVERT: p 438 ARG cc_start: 0.5177 (mpp-170) cc_final: 0.4968 (mpp-170) REVERT: p 463 ARG cc_start: 0.4523 (ttp-110) cc_final: 0.3945 (mtp180) REVERT: p 508 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.5951 (mtt) REVERT: p 546 GLU cc_start: 0.6701 (tp30) cc_final: 0.6417 (mm-30) REVERT: p 550 MET cc_start: 0.5979 (ttp) cc_final: 0.4867 (tmm) REVERT: p 551 GLU cc_start: 0.7558 (mp0) cc_final: 0.6816 (pm20) REVERT: p 597 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7653 (mm) REVERT: p 630 LYS cc_start: 0.6980 (mttt) cc_final: 0.6548 (mmtm) REVERT: p 636 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6471 (mmmt) REVERT: p 728 MET cc_start: 0.7124 (mtm) cc_final: 0.6740 (mtp) REVERT: p 733 MET cc_start: 0.8151 (ttm) cc_final: 0.7827 (ttm) REVERT: p 745 ASP cc_start: 0.6698 (m-30) cc_final: 0.6485 (m-30) REVERT: p 761 THR cc_start: 0.7844 (m) cc_final: 0.7510 (p) REVERT: p 771 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: p 796 MET cc_start: 0.8915 (mtm) cc_final: 0.8563 (mtm) REVERT: p 809 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7121 (p) REVERT: p 817 GLN cc_start: 0.7634 (tt0) cc_final: 0.6666 (pm20) REVERT: p 931 ILE cc_start: 0.7765 (pt) cc_final: 0.7375 (pp) REVERT: p 952 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: p 1054 MET cc_start: 0.8334 (mtm) cc_final: 0.7746 (mtm) REVERT: p 1080 ARG cc_start: 0.7269 (mtt90) cc_final: 0.6552 (mtp85) REVERT: p 1091 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.5162 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7766 (tp40) cc_final: 0.7272 (tt0) REVERT: p 1165 MET cc_start: 0.7966 (mtm) cc_final: 0.7627 (mtp) REVERT: p 1172 MET cc_start: 0.7660 (mmt) cc_final: 0.7215 (mmt) REVERT: q 17 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6810 (pm20) REVERT: q 41 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: q 81 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7031 (mttt) REVERT: q 94 CYS cc_start: 0.4799 (OUTLIER) cc_final: 0.4588 (p) REVERT: q 96 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7008 (mp0) REVERT: q 126 ARG cc_start: 0.7800 (mtt180) cc_final: 0.6775 (mmp-170) REVERT: q 155 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6376 (tppp) REVERT: q 158 GLU cc_start: 0.7191 (tt0) cc_final: 0.6457 (pt0) REVERT: q 199 LYS cc_start: 0.8102 (mttt) cc_final: 0.7660 (mtmm) REVERT: q 254 LYS cc_start: 0.6145 (tttt) cc_final: 0.5788 (mppt) REVERT: q 262 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6774 (mm110) REVERT: r 39 MET cc_start: 0.8339 (ptp) cc_final: 0.8097 (mpm) REVERT: s 3 ASP cc_start: 0.5609 (m-30) cc_final: 0.5328 (OUTLIER) REVERT: s 96 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8115 (tm-30) REVERT: s 98 ASN cc_start: 0.8996 (t0) cc_final: 0.8759 (t0) REVERT: s 104 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6401 (mm) REVERT: s 108 GLN cc_start: 0.7779 (mt0) cc_final: 0.7515 (tt0) REVERT: s 126 ILE cc_start: 0.7313 (mt) cc_final: 0.7013 (mp) REVERT: s 158 GLU cc_start: 0.6237 (tt0) cc_final: 0.6002 (pt0) REVERT: t 50 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6922 (pmtt) REVERT: t 57 MET cc_start: 0.7861 (ttp) cc_final: 0.7447 (ttm) REVERT: t 59 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6098 (ptmt) REVERT: u 16 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6419 (ptp-170) REVERT: u 101 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6937 (pp) REVERT: u 104 MET cc_start: 0.7451 (ttp) cc_final: 0.6722 (tmm) REVERT: v 20 LYS cc_start: 0.7414 (tttt) cc_final: 0.7031 (tptp) REVERT: v 36 LYS cc_start: 0.6306 (mmtm) cc_final: 0.5748 (mmpt) REVERT: v 51 ASP cc_start: 0.7683 (m-30) cc_final: 0.6863 (p0) REVERT: v 54 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: v 63 THR cc_start: 0.8463 (p) cc_final: 0.8100 (t) REVERT: v 100 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6077 (mt-10) REVERT: v 126 GLN cc_start: 0.7381 (tt0) cc_final: 0.7133 (tt0) REVERT: v 133 HIS cc_start: 0.7330 (m170) cc_final: 0.6926 (m-70) REVERT: v 146 LYS cc_start: 0.6719 (tttt) cc_final: 0.6266 (tttm) REVERT: w 71 ASP cc_start: 0.7813 (m-30) cc_final: 0.7463 (m-30) REVERT: x 19 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: x 41 LYS cc_start: 0.8203 (mptt) cc_final: 0.7880 (mmtm) REVERT: x 66 GLU cc_start: 0.6429 (tt0) cc_final: 0.5756 (pm20) REVERT: y 8 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6866 (mt-10) REVERT: y 16 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6298 (tt0) REVERT: y 17 LYS cc_start: 0.7396 (mtpp) cc_final: 0.7086 (mmmm) REVERT: y 23 LYS cc_start: 0.8174 (mttt) cc_final: 0.7820 (ttpp) REVERT: y 35 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7124 (mm) REVERT: y 47 LYS cc_start: 0.6666 (ttpp) cc_final: 0.6310 (tttm) REVERT: y 48 SER cc_start: 0.7972 (t) cc_final: 0.7703 (p) REVERT: y 84 GLN cc_start: 0.6770 (mp10) cc_final: 0.6348 (mp-120) REVERT: y 85 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5673 (tt0) REVERT: y 103 GLU cc_start: 0.7068 (tp30) cc_final: 0.6492 (tp30) REVERT: z 15 MET cc_start: 0.6401 (mmm) cc_final: 0.6005 (mmt) REVERT: z 16 ILE cc_start: 0.8348 (mt) cc_final: 0.7877 (mp) REVERT: z 25 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: z 38 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7911 (pm20) outliers start: 160 outliers final: 94 residues processed: 656 average time/residue: 1.6498 time to fit residues: 1286.7660 Evaluate side-chains 683 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 555 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 229 SER Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 517 GLU Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 841 MET Chi-restraints excluded: chain o residue 867 SER Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1257 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1460 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 324 ARG Chi-restraints excluded: chain p residue 336 ILE Chi-restraints excluded: chain p residue 337 LYS Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 385 ARG Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 437 THR Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 636 LYS Chi-restraints excluded: chain p residue 638 ARG Chi-restraints excluded: chain p residue 672 THR Chi-restraints excluded: chain p residue 673 VAL Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1133 HIS Chi-restraints excluded: chain p residue 1151 MET Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 59 LYS Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 100 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 0.0040 chunk 162 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 318 optimal weight: 0.0980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 765 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS q 18 ASN ** q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN z 23 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 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 : 0.004 0.047 36632 Z= 0.238 Angle : 0.456 10.175 49964 Z= 0.242 Chirality : 0.040 0.187 5568 Planarity : 0.003 0.039 6099 Dihedral : 15.961 131.132 5823 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 4.39 % Allowed : 18.82 % Favored : 76.79 % 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: 0.96 (0.13), residues: 4137 helix: 2.11 (0.14), residues: 1411 sheet: 0.16 (0.20), residues: 681 loop : -0.19 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP o 479 HIS 0.010 0.001 HIS p1133 PHE 0.016 0.001 PHE q 63 TYR 0.018 0.001 TYR q 231 ARG 0.006 0.000 ARG p 463 *********************** 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 718 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 556 time to evaluate : 4.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.6818 (mmt90) cc_final: 0.6298 (mtt-85) REVERT: o 19 LYS cc_start: 0.7227 (mmtp) cc_final: 0.7019 (tppp) REVERT: o 116 LYS cc_start: 0.7538 (mttt) cc_final: 0.6874 (mtmm) REVERT: o 120 ASP cc_start: 0.7689 (m-30) cc_final: 0.7434 (m-30) REVERT: o 136 GLN cc_start: 0.7682 (mt0) cc_final: 0.7220 (mp10) REVERT: o 192 ARG cc_start: 0.7316 (ptm160) cc_final: 0.7049 (ptt90) REVERT: o 197 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7164 (pm20) REVERT: o 219 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6796 (mp0) REVERT: o 233 CYS cc_start: 0.6265 (t) cc_final: 0.5858 (p) REVERT: o 238 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6821 (mtp) REVERT: o 271 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7501 (mmm-85) REVERT: o 272 ASN cc_start: 0.7831 (m-40) cc_final: 0.7497 (t0) REVERT: o 306 ASP cc_start: 0.7441 (m-30) cc_final: 0.7045 (m-30) REVERT: o 382 ARG cc_start: 0.6333 (mtp-110) cc_final: 0.6028 (ttm110) REVERT: o 426 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7263 (ptp-110) REVERT: o 473 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6391 (mtm-85) REVERT: o 486 LEU cc_start: 0.7371 (mt) cc_final: 0.7115 (mt) REVERT: o 514 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6383 (tt0) REVERT: o 524 MET cc_start: 0.7993 (mmp) cc_final: 0.7657 (mmm) REVERT: o 561 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7380 (mtm) REVERT: o 580 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7292 (mt) REVERT: o 612 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6893 (p0) REVERT: o 619 LYS cc_start: 0.6913 (mtpp) cc_final: 0.6625 (mttp) REVERT: o 634 GLU cc_start: 0.7339 (tt0) cc_final: 0.6658 (mt-10) REVERT: o 728 THR cc_start: 0.8010 (m) cc_final: 0.7375 (t) REVERT: o 775 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7817 (ttmm) REVERT: o 803 LYS cc_start: 0.7440 (tttp) cc_final: 0.7120 (tptp) REVERT: o 818 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7485 (mt-10) REVERT: o 861 GLN cc_start: 0.7385 (tp40) cc_final: 0.6656 (mt0) REVERT: o 867 SER cc_start: 0.6935 (OUTLIER) cc_final: 0.6686 (m) REVERT: o 876 ASP cc_start: 0.7403 (t0) cc_final: 0.6394 (t0) REVERT: o 900 SER cc_start: 0.8157 (m) cc_final: 0.7925 (t) REVERT: o 936 GLU cc_start: 0.7626 (tt0) cc_final: 0.7375 (tp30) REVERT: o 1026 ASP cc_start: 0.7871 (p0) cc_final: 0.7592 (p0) REVERT: o 1063 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6986 (mt-10) REVERT: o 1085 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6284 (tp30) REVERT: o 1104 LEU cc_start: 0.5085 (OUTLIER) cc_final: 0.4591 (mt) REVERT: o 1132 LYS cc_start: 0.8093 (mptt) cc_final: 0.7644 (mppt) REVERT: o 1135 LYS cc_start: 0.7754 (mttt) cc_final: 0.7454 (tppt) REVERT: o 1136 THR cc_start: 0.8285 (m) cc_final: 0.7969 (p) REVERT: o 1147 SER cc_start: 0.6826 (OUTLIER) cc_final: 0.6348 (t) REVERT: o 1286 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7011 (mtp85) REVERT: o 1306 LYS cc_start: 0.6151 (mttt) cc_final: 0.5680 (tttm) REVERT: o 1309 MET cc_start: 0.8574 (ptm) cc_final: 0.7848 (ttp) REVERT: o 1324 GLU cc_start: 0.6612 (mp0) cc_final: 0.6229 (tp30) REVERT: o 1337 GLU cc_start: 0.6220 (mt-10) cc_final: 0.6013 (mt-10) REVERT: o 1361 ASP cc_start: 0.7709 (t0) cc_final: 0.7344 (t0) REVERT: o 1412 MET cc_start: 0.7357 (ttp) cc_final: 0.6812 (tmm) REVERT: o 1422 GLN cc_start: 0.6703 (mt0) cc_final: 0.5559 (mm-40) REVERT: o 1423 ASP cc_start: 0.8021 (m-30) cc_final: 0.7175 (t0) REVERT: o 1452 LYS cc_start: 0.7422 (mttt) cc_final: 0.6767 (mptt) REVERT: o 1460 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6943 (mp) REVERT: o 1472 ASP cc_start: 0.7437 (t0) cc_final: 0.6754 (t0) REVERT: p 49 GLU cc_start: 0.6358 (tp30) cc_final: 0.5829 (tp30) REVERT: p 53 MET cc_start: 0.6459 (mmm) cc_final: 0.5688 (mmm) REVERT: p 57 ARG cc_start: 0.5274 (ttp-110) cc_final: 0.4720 (mtt90) REVERT: p 168 ASP cc_start: 0.5687 (p0) cc_final: 0.5398 (m-30) REVERT: p 222 ARG cc_start: 0.6220 (mtp-110) cc_final: 0.5830 (mtp85) REVERT: p 300 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8017 (mmm) REVERT: p 324 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.5874 (mmm-85) REVERT: p 334 LYS cc_start: 0.8003 (tttt) cc_final: 0.7589 (tptt) REVERT: p 335 ARG cc_start: 0.6339 (mtm180) cc_final: 0.5927 (mtm-85) REVERT: p 336 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.6428 (mt) REVERT: p 358 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6648 (pm20) REVERT: p 381 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7532 (mp0) REVERT: p 385 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6113 (ttm-80) REVERT: p 386 ASP cc_start: 0.7728 (m-30) cc_final: 0.6966 (m-30) REVERT: p 416 ARG cc_start: 0.6105 (mmm-85) cc_final: 0.5788 (ttp80) REVERT: p 438 ARG cc_start: 0.5176 (mpp-170) cc_final: 0.4966 (mpp-170) REVERT: p 508 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.5972 (mtt) REVERT: p 546 GLU cc_start: 0.6718 (tp30) cc_final: 0.6464 (mm-30) REVERT: p 550 MET cc_start: 0.5994 (ttp) cc_final: 0.5023 (tmm) REVERT: p 551 GLU cc_start: 0.7424 (mp0) cc_final: 0.6684 (pm20) REVERT: p 592 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.4224 (mpt90) REVERT: p 597 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7616 (mp) REVERT: p 606 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6561 (t0) REVERT: p 630 LYS cc_start: 0.6986 (mttt) cc_final: 0.6578 (mmtm) REVERT: p 636 LYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6466 (mmmt) REVERT: p 728 MET cc_start: 0.7186 (mtm) cc_final: 0.6790 (mtp) REVERT: p 733 MET cc_start: 0.8151 (ttm) cc_final: 0.7812 (ttm) REVERT: p 745 ASP cc_start: 0.7289 (m-30) cc_final: 0.7080 (m-30) REVERT: p 761 THR cc_start: 0.7873 (m) cc_final: 0.7525 (p) REVERT: p 771 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: p 796 MET cc_start: 0.8930 (mtm) cc_final: 0.8571 (mtm) REVERT: p 809 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7131 (p) REVERT: p 817 GLN cc_start: 0.7648 (tt0) cc_final: 0.6656 (pm20) REVERT: p 931 ILE cc_start: 0.7817 (pt) cc_final: 0.7439 (pp) REVERT: p 952 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: p 1054 MET cc_start: 0.8332 (mtm) cc_final: 0.7775 (mtm) REVERT: p 1080 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6507 (mtp85) REVERT: p 1091 ARG cc_start: 0.5633 (OUTLIER) cc_final: 0.5247 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7776 (tp40) cc_final: 0.7278 (tt0) REVERT: p 1165 MET cc_start: 0.7973 (mtm) cc_final: 0.7651 (mtp) REVERT: p 1172 MET cc_start: 0.7645 (mmt) cc_final: 0.7185 (mmt) REVERT: q 17 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6815 (pm20) REVERT: q 41 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: q 81 LYS cc_start: 0.7654 (mtpt) cc_final: 0.7041 (mttt) REVERT: q 96 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6918 (mp0) REVERT: q 126 ARG cc_start: 0.7792 (mtt180) cc_final: 0.6738 (mmp-170) REVERT: q 155 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.6550 (tppp) REVERT: q 158 GLU cc_start: 0.7309 (tt0) cc_final: 0.6639 (pt0) REVERT: q 199 LYS cc_start: 0.8106 (mttt) cc_final: 0.7660 (mtmm) REVERT: q 254 LYS cc_start: 0.6148 (tttt) cc_final: 0.5792 (mppt) REVERT: q 262 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6795 (mm110) REVERT: r 39 MET cc_start: 0.8345 (ptp) cc_final: 0.8073 (mpm) REVERT: s 3 ASP cc_start: 0.5618 (m-30) cc_final: 0.5340 (OUTLIER) REVERT: s 95 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8803 (pp30) REVERT: s 98 ASN cc_start: 0.9027 (t0) cc_final: 0.8812 (t0) REVERT: s 104 ILE cc_start: 0.6704 (OUTLIER) cc_final: 0.6416 (mm) REVERT: s 126 ILE cc_start: 0.7328 (mt) cc_final: 0.7006 (mp) REVERT: s 158 GLU cc_start: 0.6240 (tt0) cc_final: 0.6002 (pt0) REVERT: t 50 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6929 (pmtt) REVERT: t 57 MET cc_start: 0.7869 (ttp) cc_final: 0.7452 (ttm) REVERT: t 59 LYS cc_start: 0.6435 (OUTLIER) cc_final: 0.6108 (ptmt) REVERT: u 16 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6338 (ptp-170) REVERT: u 101 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6890 (pp) REVERT: u 104 MET cc_start: 0.7456 (ttp) cc_final: 0.6735 (tmm) REVERT: v 20 LYS cc_start: 0.7410 (tttt) cc_final: 0.7019 (tptp) REVERT: v 36 LYS cc_start: 0.6171 (mmtm) cc_final: 0.5642 (mmpt) REVERT: v 37 MET cc_start: 0.7614 (mtp) cc_final: 0.7160 (mmm) REVERT: v 38 ASP cc_start: 0.7275 (m-30) cc_final: 0.6930 (m-30) REVERT: v 51 ASP cc_start: 0.7573 (m-30) cc_final: 0.6776 (p0) REVERT: v 57 ARG cc_start: 0.7277 (ttp80) cc_final: 0.6918 (ttp80) REVERT: v 63 THR cc_start: 0.8459 (p) cc_final: 0.8096 (t) REVERT: v 100 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6063 (mt-10) REVERT: v 133 HIS cc_start: 0.7274 (m170) cc_final: 0.6874 (m-70) REVERT: v 146 LYS cc_start: 0.6729 (tttt) cc_final: 0.6251 (tttm) REVERT: w 71 ASP cc_start: 0.7769 (m-30) cc_final: 0.7458 (m-30) REVERT: x 19 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: x 41 LYS cc_start: 0.8190 (mptt) cc_final: 0.7875 (mmtm) REVERT: x 66 GLU cc_start: 0.6435 (tt0) cc_final: 0.5823 (pm20) REVERT: y 8 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6890 (mt-10) REVERT: y 16 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6313 (tt0) REVERT: y 17 LYS cc_start: 0.7415 (mtpp) cc_final: 0.7135 (mmmm) REVERT: y 23 LYS cc_start: 0.8147 (mttt) cc_final: 0.7695 (mptt) REVERT: y 35 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7098 (mm) REVERT: y 47 LYS cc_start: 0.6674 (ttpp) cc_final: 0.6324 (tttm) REVERT: y 48 SER cc_start: 0.7982 (t) cc_final: 0.7712 (p) REVERT: y 84 GLN cc_start: 0.6829 (mp10) cc_final: 0.6497 (mp-120) REVERT: y 85 GLU cc_start: 0.6332 (mt-10) cc_final: 0.5674 (tt0) REVERT: y 103 GLU cc_start: 0.7077 (tp30) cc_final: 0.6501 (tp30) REVERT: z 15 MET cc_start: 0.6330 (mmm) cc_final: 0.6017 (mmt) REVERT: z 16 ILE cc_start: 0.8324 (mt) cc_final: 0.7889 (mp) REVERT: z 25 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: z 38 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7923 (pm20) outliers start: 162 outliers final: 103 residues processed: 654 average time/residue: 1.6689 time to fit residues: 1295.5570 Evaluate side-chains 685 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 546 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 229 SER Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 517 GLU Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 841 MET Chi-restraints excluded: chain o residue 867 SER 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 1140 THR Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1257 LEU Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1460 LEU Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 324 ARG Chi-restraints excluded: chain p residue 336 ILE Chi-restraints excluded: chain p residue 337 LYS Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 385 ARG Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 437 THR Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 592 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 636 LYS Chi-restraints excluded: chain p residue 638 ARG Chi-restraints excluded: chain p residue 672 THR Chi-restraints excluded: chain p residue 673 VAL Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1104 ARG Chi-restraints excluded: chain p residue 1118 VAL Chi-restraints excluded: chain p residue 1151 MET Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 59 LYS Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 69 THR Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 100 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 40.0000 chunk 388 optimal weight: 0.5980 chunk 354 optimal weight: 2.9990 chunk 378 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 296 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 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** ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36632 Z= 0.197 Angle : 0.439 10.072 49964 Z= 0.234 Chirality : 0.039 0.173 5568 Planarity : 0.003 0.043 6099 Dihedral : 15.868 128.435 5823 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 3.96 % Allowed : 19.12 % Favored : 76.93 % 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: 1.03 (0.13), residues: 4137 helix: 2.19 (0.14), residues: 1410 sheet: 0.20 (0.20), residues: 680 loop : -0.17 (0.14), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP o 679 HIS 0.007 0.001 HIS r 43 PHE 0.023 0.001 PHE o 234 TYR 0.017 0.001 TYR t 115 ARG 0.009 0.000 ARG p 463 *********************** 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 690 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 544 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.6824 (mmt90) cc_final: 0.6297 (mtt-85) REVERT: o 116 LYS cc_start: 0.7537 (mttt) cc_final: 0.6861 (mtmm) REVERT: o 120 ASP cc_start: 0.7701 (m-30) cc_final: 0.7442 (m-30) REVERT: o 136 GLN cc_start: 0.7562 (mt0) cc_final: 0.7079 (mp10) REVERT: o 192 ARG cc_start: 0.7304 (ptm160) cc_final: 0.7029 (ptt90) REVERT: o 197 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7115 (pm20) REVERT: o 219 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6791 (mp0) REVERT: o 233 CYS cc_start: 0.6425 (t) cc_final: 0.6039 (p) REVERT: o 238 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6840 (mtp) REVERT: o 271 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7508 (mmm-85) REVERT: o 272 ASN cc_start: 0.7831 (m-40) cc_final: 0.7489 (t0) REVERT: o 305 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6995 (mm-30) REVERT: o 306 ASP cc_start: 0.7458 (m-30) cc_final: 0.7088 (m-30) REVERT: o 382 ARG cc_start: 0.6339 (mtp-110) cc_final: 0.6031 (ttm110) REVERT: o 426 ARG cc_start: 0.7842 (mtm180) cc_final: 0.7283 (ptp-110) REVERT: o 473 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6442 (mtm-85) REVERT: o 486 LEU cc_start: 0.7267 (mt) cc_final: 0.7010 (mt) REVERT: o 514 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6376 (tt0) REVERT: o 524 MET cc_start: 0.8000 (mmp) cc_final: 0.7533 (mmm) REVERT: o 561 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7319 (mtm) REVERT: o 580 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7279 (mt) REVERT: o 612 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6916 (p0) REVERT: o 619 LYS cc_start: 0.7156 (mtpp) cc_final: 0.6808 (mttp) REVERT: o 634 GLU cc_start: 0.7301 (tt0) cc_final: 0.6670 (mt-10) REVERT: o 775 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7876 (ttmm) REVERT: o 803 LYS cc_start: 0.7462 (tttp) cc_final: 0.7128 (tptp) REVERT: o 818 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7194 (mp0) REVERT: o 861 GLN cc_start: 0.7252 (tp40) cc_final: 0.6643 (mt0) REVERT: o 867 SER cc_start: 0.6757 (OUTLIER) cc_final: 0.6473 (m) REVERT: o 876 ASP cc_start: 0.7371 (t0) cc_final: 0.6449 (t0) REVERT: o 899 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6532 (mp0) REVERT: o 900 SER cc_start: 0.8154 (m) cc_final: 0.7906 (t) REVERT: o 936 GLU cc_start: 0.7646 (tt0) cc_final: 0.7417 (tp30) REVERT: o 1026 ASP cc_start: 0.7898 (p0) cc_final: 0.7612 (p0) REVERT: o 1063 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6952 (mt-10) REVERT: o 1085 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6306 (tp30) REVERT: o 1132 LYS cc_start: 0.8099 (mptt) cc_final: 0.7643 (mppt) REVERT: o 1135 LYS cc_start: 0.7756 (mttt) cc_final: 0.7450 (tppt) REVERT: o 1136 THR cc_start: 0.8270 (m) cc_final: 0.7954 (p) REVERT: o 1147 SER cc_start: 0.6582 (OUTLIER) cc_final: 0.6194 (t) REVERT: o 1219 LYS cc_start: 0.8505 (tppt) cc_final: 0.8290 (tppt) REVERT: o 1286 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7024 (mtp85) REVERT: o 1306 LYS cc_start: 0.6149 (mttt) cc_final: 0.5694 (tttm) REVERT: o 1309 MET cc_start: 0.8577 (ptm) cc_final: 0.7824 (ttp) REVERT: o 1324 GLU cc_start: 0.6655 (mp0) cc_final: 0.6282 (tp30) REVERT: o 1337 GLU cc_start: 0.6234 (mt-10) cc_final: 0.6024 (mt-10) REVERT: o 1361 ASP cc_start: 0.7852 (t0) cc_final: 0.7458 (t0) REVERT: o 1412 MET cc_start: 0.7351 (ttp) cc_final: 0.6814 (tmm) REVERT: o 1422 GLN cc_start: 0.6678 (mt0) cc_final: 0.5595 (mm-40) REVERT: o 1452 LYS cc_start: 0.7415 (mttt) cc_final: 0.6749 (mptt) REVERT: o 1460 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6904 (mp) REVERT: o 1472 ASP cc_start: 0.7399 (t0) cc_final: 0.6773 (t0) REVERT: p 49 GLU cc_start: 0.6330 (tp30) cc_final: 0.5823 (tp30) REVERT: p 53 MET cc_start: 0.6456 (mmm) cc_final: 0.5803 (mmm) REVERT: p 57 ARG cc_start: 0.5282 (ttp-110) cc_final: 0.4832 (mtt90) REVERT: p 168 ASP cc_start: 0.5692 (p0) cc_final: 0.5396 (m-30) REVERT: p 222 ARG cc_start: 0.6205 (mtp-110) cc_final: 0.5804 (mtp85) REVERT: p 324 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.5857 (mmm-85) REVERT: p 334 LYS cc_start: 0.8007 (tttt) cc_final: 0.7595 (tptt) REVERT: p 335 ARG cc_start: 0.6329 (mtm180) cc_final: 0.5919 (mtm-85) REVERT: p 336 ILE cc_start: 0.6639 (OUTLIER) cc_final: 0.6381 (mt) REVERT: p 381 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7527 (mp0) REVERT: p 385 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6119 (ttm-80) REVERT: p 386 ASP cc_start: 0.7726 (m-30) cc_final: 0.6951 (m-30) REVERT: p 416 ARG cc_start: 0.6099 (mmm-85) cc_final: 0.5786 (ttp80) REVERT: p 438 ARG cc_start: 0.5164 (mpp-170) cc_final: 0.4950 (mpp-170) REVERT: p 508 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.6542 (mtt) REVERT: p 546 GLU cc_start: 0.6718 (tp30) cc_final: 0.6468 (mm-30) REVERT: p 550 MET cc_start: 0.6029 (ttp) cc_final: 0.5070 (tmm) REVERT: p 551 GLU cc_start: 0.7411 (mp0) cc_final: 0.6668 (pm20) REVERT: p 592 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.4350 (mpt90) REVERT: p 606 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6544 (t0) REVERT: p 636 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6462 (mmmt) REVERT: p 728 MET cc_start: 0.7166 (mtm) cc_final: 0.6775 (mtp) REVERT: p 733 MET cc_start: 0.8134 (ttm) cc_final: 0.7778 (ttm) REVERT: p 745 ASP cc_start: 0.7186 (m-30) cc_final: 0.6970 (m-30) REVERT: p 761 THR cc_start: 0.7841 (m) cc_final: 0.7502 (p) REVERT: p 771 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: p 796 MET cc_start: 0.8927 (mtm) cc_final: 0.8582 (mtm) REVERT: p 809 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7144 (p) REVERT: p 817 GLN cc_start: 0.7812 (tt0) cc_final: 0.6735 (pm20) REVERT: p 931 ILE cc_start: 0.7812 (pt) cc_final: 0.7444 (pp) REVERT: p 952 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: p 1041 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8077 (mp) REVERT: p 1054 MET cc_start: 0.8321 (mtm) cc_final: 0.7757 (mtm) REVERT: p 1080 ARG cc_start: 0.7259 (mtt90) cc_final: 0.6530 (mtp85) REVERT: p 1091 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5219 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7770 (tp40) cc_final: 0.7273 (tt0) REVERT: p 1165 MET cc_start: 0.7974 (mtm) cc_final: 0.7646 (mtp) REVERT: p 1172 MET cc_start: 0.7635 (mmt) cc_final: 0.7172 (mmt) REVERT: q 17 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6805 (pm20) REVERT: q 41 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: q 81 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7043 (mttt) REVERT: q 126 ARG cc_start: 0.7796 (mtt180) cc_final: 0.6739 (mmp-170) REVERT: q 155 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6407 (tppp) REVERT: q 158 GLU cc_start: 0.7315 (tt0) cc_final: 0.6614 (pt0) REVERT: q 199 LYS cc_start: 0.8100 (mttt) cc_final: 0.7648 (mtmm) REVERT: q 254 LYS cc_start: 0.6135 (tttt) cc_final: 0.5783 (mppt) REVERT: q 262 GLN cc_start: 0.7051 (mm-40) cc_final: 0.6792 (mm110) REVERT: s 3 ASP cc_start: 0.5598 (m-30) cc_final: 0.5328 (OUTLIER) REVERT: s 95 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8779 (pp30) REVERT: s 98 ASN cc_start: 0.9026 (t0) cc_final: 0.8812 (t0) REVERT: s 158 GLU cc_start: 0.6232 (tt0) cc_final: 0.5992 (pt0) REVERT: t 50 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6890 (pmtt) REVERT: t 57 MET cc_start: 0.7866 (ttp) cc_final: 0.7469 (ttm) REVERT: t 59 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.6181 (ptmt) REVERT: u 16 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6373 (ptp-170) REVERT: u 104 MET cc_start: 0.7440 (ttp) cc_final: 0.6670 (tmm) REVERT: v 20 LYS cc_start: 0.7466 (tttt) cc_final: 0.7083 (tptp) REVERT: v 36 LYS cc_start: 0.6009 (mmtm) cc_final: 0.5514 (mmpt) REVERT: v 37 MET cc_start: 0.7573 (mtp) cc_final: 0.7263 (mmm) REVERT: v 38 ASP cc_start: 0.7151 (m-30) cc_final: 0.6657 (m-30) REVERT: v 51 ASP cc_start: 0.7582 (m-30) cc_final: 0.6767 (p0) REVERT: v 57 ARG cc_start: 0.7286 (ttp80) cc_final: 0.6924 (ttp80) REVERT: v 63 THR cc_start: 0.8466 (p) cc_final: 0.8098 (t) REVERT: v 100 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6091 (mt-10) REVERT: v 133 HIS cc_start: 0.7358 (m170) cc_final: 0.6957 (m-70) REVERT: v 146 LYS cc_start: 0.6730 (tttt) cc_final: 0.6249 (tttm) REVERT: w 28 GLU cc_start: 0.6390 (tt0) cc_final: 0.6189 (tt0) REVERT: w 71 ASP cc_start: 0.7669 (m-30) cc_final: 0.7340 (m-30) REVERT: x 19 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: x 66 GLU cc_start: 0.6409 (tt0) cc_final: 0.5826 (pm20) REVERT: y 8 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6890 (mt-10) REVERT: y 16 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: y 17 LYS cc_start: 0.7437 (mtpp) cc_final: 0.7138 (mmmm) REVERT: y 23 LYS cc_start: 0.8107 (mttt) cc_final: 0.7670 (mptt) REVERT: y 35 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7090 (mm) REVERT: y 47 LYS cc_start: 0.6655 (ttpp) cc_final: 0.6316 (tttm) REVERT: y 48 SER cc_start: 0.7974 (t) cc_final: 0.7708 (p) REVERT: y 84 GLN cc_start: 0.6758 (mp10) cc_final: 0.6417 (mp-120) REVERT: y 85 GLU cc_start: 0.6305 (mt-10) cc_final: 0.5683 (tt0) REVERT: y 103 GLU cc_start: 0.7250 (tp30) cc_final: 0.6647 (tp30) REVERT: z 15 MET cc_start: 0.6326 (mmm) cc_final: 0.6010 (mmt) REVERT: z 16 ILE cc_start: 0.8325 (mt) cc_final: 0.7893 (mp) REVERT: z 25 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: z 38 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7915 (pm20) outliers start: 146 outliers final: 88 residues processed: 643 average time/residue: 1.6937 time to fit residues: 1292.3449 Evaluate side-chains 658 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 537 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 229 SER Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 517 GLU Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 867 SER Chi-restraints excluded: chain o residue 899 GLU Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1257 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1460 LEU Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 324 ARG Chi-restraints excluded: chain p residue 336 ILE Chi-restraints excluded: chain p residue 385 ARG Chi-restraints excluded: chain p residue 390 ASN Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 437 THR Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 592 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 636 LYS Chi-restraints excluded: chain p residue 638 ARG Chi-restraints excluded: chain p residue 672 THR Chi-restraints excluded: chain p residue 673 VAL Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1104 ARG Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 117 SER Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 59 LYS Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 100 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.0010 chunk 399 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 277 optimal weight: 0.7980 chunk 419 optimal weight: 3.9990 chunk 386 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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** ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 98 HIS ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36632 Z= 0.267 Angle : 0.478 10.299 49964 Z= 0.253 Chirality : 0.040 0.177 5568 Planarity : 0.003 0.043 6099 Dihedral : 15.870 126.355 5823 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 28.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.80 % Rotamer: Outliers : 3.80 % Allowed : 19.44 % Favored : 76.76 % 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: 2.03 (0.14), residues: 1409 sheet: 0.15 (0.20), residues: 691 loop : -0.26 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 479 HIS 0.007 0.001 HIS r 43 PHE 0.017 0.001 PHE q 63 TYR 0.020 0.001 TYR q 231 ARG 0.009 0.000 ARG p 463 ********************** 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 687 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 547 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.6822 (mmt90) cc_final: 0.6289 (mtt-85) REVERT: o 66 GLU cc_start: 0.7613 (pm20) cc_final: 0.7067 (pm20) REVERT: o 116 LYS cc_start: 0.7531 (mttt) cc_final: 0.6855 (mtmm) REVERT: o 120 ASP cc_start: 0.7658 (m-30) cc_final: 0.7407 (m-30) REVERT: o 136 GLN cc_start: 0.7687 (mt0) cc_final: 0.7188 (mp10) REVERT: o 192 ARG cc_start: 0.7284 (ptm160) cc_final: 0.6982 (ptt90) REVERT: o 197 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7108 (pm20) REVERT: o 219 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6801 (mp0) REVERT: o 233 CYS cc_start: 0.6341 (t) cc_final: 0.5878 (p) REVERT: o 238 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6853 (mtp) REVERT: o 271 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7608 (mmm-85) REVERT: o 272 ASN cc_start: 0.7865 (m-40) cc_final: 0.7530 (t0) REVERT: o 305 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6912 (mm-30) REVERT: o 306 ASP cc_start: 0.7412 (m-30) cc_final: 0.7099 (m-30) REVERT: o 382 ARG cc_start: 0.6338 (mtp-110) cc_final: 0.6016 (ttm110) REVERT: o 426 ARG cc_start: 0.7861 (mtm180) cc_final: 0.7297 (ptp-110) REVERT: o 473 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6417 (mtm-85) REVERT: o 486 LEU cc_start: 0.7397 (mt) cc_final: 0.7146 (mt) REVERT: o 514 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6289 (tt0) REVERT: o 524 MET cc_start: 0.7884 (mmp) cc_final: 0.7558 (mmm) REVERT: o 561 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7388 (mtm) REVERT: o 580 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7332 (mt) REVERT: o 612 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6928 (p0) REVERT: o 634 GLU cc_start: 0.7355 (tt0) cc_final: 0.6648 (mt-10) REVERT: o 775 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7826 (ttmm) REVERT: o 803 LYS cc_start: 0.7887 (tttp) cc_final: 0.7519 (tptp) REVERT: o 818 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7233 (mp0) REVERT: o 861 GLN cc_start: 0.7272 (tp40) cc_final: 0.6553 (mt0) REVERT: o 867 SER cc_start: 0.6935 (OUTLIER) cc_final: 0.6676 (m) REVERT: o 876 ASP cc_start: 0.7387 (t0) cc_final: 0.6491 (t0) REVERT: o 900 SER cc_start: 0.8181 (m) cc_final: 0.7960 (t) REVERT: o 936 GLU cc_start: 0.7654 (tt0) cc_final: 0.7419 (tp30) REVERT: o 1026 ASP cc_start: 0.7918 (p0) cc_final: 0.7633 (p0) REVERT: o 1063 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6991 (mt-10) REVERT: o 1085 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6291 (tp30) REVERT: o 1132 LYS cc_start: 0.8101 (mptt) cc_final: 0.7650 (mppt) REVERT: o 1135 LYS cc_start: 0.7770 (mttt) cc_final: 0.7457 (tppt) REVERT: o 1136 THR cc_start: 0.8273 (m) cc_final: 0.7960 (p) REVERT: o 1147 SER cc_start: 0.6601 (OUTLIER) cc_final: 0.6264 (t) REVERT: o 1219 LYS cc_start: 0.8519 (tppt) cc_final: 0.8306 (tppt) REVERT: o 1286 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.7062 (mtp85) REVERT: o 1306 LYS cc_start: 0.6149 (mttt) cc_final: 0.5690 (tttm) REVERT: o 1309 MET cc_start: 0.8593 (ptm) cc_final: 0.7777 (ttp) REVERT: o 1324 GLU cc_start: 0.6652 (mp0) cc_final: 0.6246 (tp30) REVERT: o 1337 GLU cc_start: 0.6225 (mt-10) cc_final: 0.6023 (mt-10) REVERT: o 1361 ASP cc_start: 0.7636 (t0) cc_final: 0.7227 (t0) REVERT: o 1412 MET cc_start: 0.7347 (ttp) cc_final: 0.6805 (tmm) REVERT: o 1422 GLN cc_start: 0.6696 (mt0) cc_final: 0.5611 (mm-40) REVERT: o 1452 LYS cc_start: 0.7449 (mttt) cc_final: 0.6781 (mptt) REVERT: o 1460 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6912 (mp) REVERT: p 49 GLU cc_start: 0.6316 (tp30) cc_final: 0.5878 (tp30) REVERT: p 53 MET cc_start: 0.6483 (mmm) cc_final: 0.5718 (mmm) REVERT: p 57 ARG cc_start: 0.5299 (ttp-110) cc_final: 0.4725 (mtt90) REVERT: p 168 ASP cc_start: 0.5674 (p0) cc_final: 0.5264 (m-30) REVERT: p 222 ARG cc_start: 0.6145 (mtp-110) cc_final: 0.5746 (mtp85) REVERT: p 265 GLN cc_start: 0.8626 (pt0) cc_final: 0.8268 (pt0) REVERT: p 300 MET cc_start: 0.8277 (mtp) cc_final: 0.8000 (mtp) REVERT: p 324 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.5959 (mmm-85) REVERT: p 334 LYS cc_start: 0.8030 (tttt) cc_final: 0.7648 (tptt) REVERT: p 335 ARG cc_start: 0.6339 (mtm180) cc_final: 0.5919 (mtm-85) REVERT: p 336 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6450 (mt) REVERT: p 381 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7527 (mp0) REVERT: p 385 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6131 (ttm-80) REVERT: p 386 ASP cc_start: 0.7716 (m-30) cc_final: 0.6965 (m-30) REVERT: p 416 ARG cc_start: 0.6146 (mmm-85) cc_final: 0.5817 (ttp80) REVERT: p 508 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.6009 (mtt) REVERT: p 550 MET cc_start: 0.6078 (ttp) cc_final: 0.5123 (tmm) REVERT: p 551 GLU cc_start: 0.7419 (mp0) cc_final: 0.6679 (pm20) REVERT: p 592 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5982 (mpt-90) REVERT: p 597 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7530 (mp) REVERT: p 606 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6498 (t0) REVERT: p 636 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6489 (mmmt) REVERT: p 728 MET cc_start: 0.7215 (mtm) cc_final: 0.6822 (mtp) REVERT: p 733 MET cc_start: 0.8089 (ttm) cc_final: 0.7792 (ttm) REVERT: p 745 ASP cc_start: 0.7556 (m-30) cc_final: 0.7325 (m-30) REVERT: p 761 THR cc_start: 0.7886 (m) cc_final: 0.7519 (p) REVERT: p 771 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: p 796 MET cc_start: 0.8946 (mtm) cc_final: 0.8588 (mtm) REVERT: p 809 VAL cc_start: 0.7722 (OUTLIER) cc_final: 0.7204 (p) REVERT: p 817 GLN cc_start: 0.7654 (tt0) cc_final: 0.6672 (pm20) REVERT: p 830 GLU cc_start: 0.7105 (pt0) cc_final: 0.6819 (tp30) REVERT: p 931 ILE cc_start: 0.7840 (pt) cc_final: 0.7458 (pp) REVERT: p 952 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: p 1054 MET cc_start: 0.8376 (mtm) cc_final: 0.7839 (mtm) REVERT: p 1080 ARG cc_start: 0.7282 (mtt90) cc_final: 0.6534 (mtp85) REVERT: p 1091 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.5319 (ptm-80) REVERT: p 1101 GLN cc_start: 0.7769 (tp40) cc_final: 0.7257 (tt0) REVERT: p 1165 MET cc_start: 0.7970 (mtm) cc_final: 0.7648 (mtp) REVERT: p 1172 MET cc_start: 0.7603 (mmt) cc_final: 0.7110 (mmt) REVERT: q 17 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6810 (pm20) REVERT: q 41 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: q 81 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7060 (mttt) REVERT: q 126 ARG cc_start: 0.7729 (mtt180) cc_final: 0.6703 (mmp-170) REVERT: q 155 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6476 (tppp) REVERT: q 158 GLU cc_start: 0.7345 (tt0) cc_final: 0.6595 (pt0) REVERT: q 199 LYS cc_start: 0.8111 (mttt) cc_final: 0.7649 (mtmm) REVERT: q 254 LYS cc_start: 0.6163 (tttt) cc_final: 0.5802 (mppt) REVERT: q 262 GLN cc_start: 0.7069 (mm-40) cc_final: 0.6795 (mm110) REVERT: s 3 ASP cc_start: 0.5579 (m-30) cc_final: 0.5301 (OUTLIER) REVERT: s 95 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8774 (pp30) REVERT: s 158 GLU cc_start: 0.6247 (tt0) cc_final: 0.6006 (pt0) REVERT: t 50 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7158 (pmtt) REVERT: t 57 MET cc_start: 0.7832 (ttp) cc_final: 0.7418 (ttm) REVERT: t 59 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.6119 (ptmt) REVERT: t 82 GLU cc_start: 0.8276 (pm20) cc_final: 0.8017 (pm20) REVERT: t 84 GLU cc_start: 0.8554 (mm-30) cc_final: 0.7744 (mp0) REVERT: u 16 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6281 (ptp-170) REVERT: v 20 LYS cc_start: 0.7467 (tttt) cc_final: 0.7053 (tptp) REVERT: v 37 MET cc_start: 0.7624 (mtp) cc_final: 0.7289 (mmm) REVERT: v 38 ASP cc_start: 0.7275 (m-30) cc_final: 0.6778 (m-30) REVERT: v 51 ASP cc_start: 0.7590 (m-30) cc_final: 0.6766 (p0) REVERT: v 63 THR cc_start: 0.8464 (p) cc_final: 0.8088 (t) REVERT: v 100 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6052 (mt-10) REVERT: v 133 HIS cc_start: 0.7297 (m170) cc_final: 0.6888 (m-70) REVERT: v 146 LYS cc_start: 0.6730 (tttt) cc_final: 0.6270 (tttm) REVERT: w 28 GLU cc_start: 0.6454 (tt0) cc_final: 0.6216 (tt0) REVERT: w 71 ASP cc_start: 0.7748 (m-30) cc_final: 0.7441 (m-30) REVERT: w 93 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6585 (tp30) REVERT: x 19 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: x 66 GLU cc_start: 0.6367 (tt0) cc_final: 0.5819 (pm20) REVERT: y 8 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6919 (mt-10) REVERT: y 16 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6170 (tt0) REVERT: y 17 LYS cc_start: 0.7459 (mtpp) cc_final: 0.7191 (mmmm) REVERT: y 23 LYS cc_start: 0.8129 (mttt) cc_final: 0.7719 (mptt) REVERT: y 35 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7077 (mm) REVERT: y 47 LYS cc_start: 0.6679 (ttpp) cc_final: 0.6341 (tttm) REVERT: y 48 SER cc_start: 0.7997 (t) cc_final: 0.7718 (p) REVERT: y 84 GLN cc_start: 0.6834 (mp10) cc_final: 0.6495 (mp-120) REVERT: y 85 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5822 (tt0) REVERT: y 103 GLU cc_start: 0.7256 (tp30) cc_final: 0.6655 (tp30) REVERT: z 15 MET cc_start: 0.6322 (mmm) cc_final: 0.6010 (mmt) REVERT: z 16 ILE cc_start: 0.8323 (mt) cc_final: 0.7924 (mp) REVERT: z 25 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: z 37 ARG cc_start: 0.7491 (ptt180) cc_final: 0.7156 (ptt180) REVERT: z 38 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7977 (pm20) outliers start: 140 outliers final: 91 residues processed: 641 average time/residue: 1.6215 time to fit residues: 1233.6644 Evaluate side-chains 663 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 540 time to evaluate : 4.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 103 THR Chi-restraints excluded: chain o residue 109 CYS Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 229 SER Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 517 GLU Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 580 LEU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 751 LYS Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 841 MET Chi-restraints excluded: chain o residue 867 SER 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 1128 ILE Chi-restraints excluded: chain o residue 1140 THR Chi-restraints excluded: chain o residue 1147 SER Chi-restraints excluded: chain o residue 1185 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1257 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1302 GLU Chi-restraints excluded: chain o residue 1325 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1460 LEU Chi-restraints excluded: chain p residue 18 THR Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 279 VAL Chi-restraints excluded: chain p residue 324 ARG Chi-restraints excluded: chain p residue 336 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 385 ARG Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 412 LEU Chi-restraints excluded: chain p residue 437 THR Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 487 SER Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 592 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 636 LYS Chi-restraints excluded: chain p residue 638 ARG Chi-restraints excluded: chain p residue 672 THR Chi-restraints excluded: chain p residue 673 VAL Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 771 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1028 LEU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1091 ARG Chi-restraints excluded: chain p residue 1151 MET Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain q residue 172 GLU Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 59 LYS Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 100 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 35 ILE Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 25 GLU Chi-restraints excluded: chain z residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 334 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 449 HIS o 485 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1101 GLN ** o1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 56 GLN p 98 HIS ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 312 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 500 GLN p 718 GLN p 749 HIS ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS q 66 HIS ** q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN z 23 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.172668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109180 restraints weight = 42633.424| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.40 r_work: 0.3148 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 36632 Z= 0.521 Angle : 0.623 10.660 49964 Z= 0.325 Chirality : 0.046 0.198 5568 Planarity : 0.005 0.059 6099 Dihedral : 16.024 124.498 5823 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 28.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % Rotamer: Outliers : 4.01 % Allowed : 19.44 % Favored : 76.55 % 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: 0.26 (0.13), residues: 4137 helix: 1.41 (0.14), residues: 1396 sheet: -0.02 (0.19), residues: 693 loop : -0.59 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP p 99 HIS 0.008 0.002 HIS o 96 PHE 0.029 0.002 PHE o 234 TYR 0.030 0.002 TYR q 231 ARG 0.009 0.001 ARG v 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19101.19 seconds wall clock time: 336 minutes 6.49 seconds (20166.49 seconds total)