Starting phenix.real_space_refine on Sat Mar 23 05:31:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wb0_37411/03_2024/8wb0_37411_trim_updated.pdb" } resolution = 2.94 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= 0.089 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 6278 2.21 5 O 6959 1.98 5 H 23 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s 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: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 876 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1115 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 71 113.941 112.485 115.214 1.00141.57 S ATOM 4761 SG CYS o 74 111.711 115.446 115.192 1.00137.29 S ATOM 4808 SG CYS o 81 110.251 111.865 114.914 1.00138.71 S ATOM 5043 SG CYS o 111 101.567 111.250 68.320 1.00164.45 S ATOM 5071 SG CYS o 114 103.654 114.590 68.072 1.00163.67 S ATOM 5417 SG CYS o 184 103.738 111.946 65.255 1.00171.81 S ATOM 24504 SG CYS p1119 105.478 124.976 104.005 1.00141.59 S ATOM 24526 SG CYS p1122 105.474 121.786 101.841 1.00142.57 S ATOM 24641 SG CYS p1137 108.317 122.515 103.987 1.00148.67 S ATOM 24662 SG CYS p1140 107.791 124.338 100.708 1.00152.98 S ATOM 25628 SG CYS q 88 85.525 90.731 173.418 1.00138.12 S ATOM 25641 SG CYS q 90 89.001 89.804 172.365 1.00147.15 S ATOM 25676 SG CYS q 94 87.158 87.447 174.624 1.00132.97 S ATOM 25698 SG CYS q 97 85.749 87.770 171.215 1.00132.45 S ATOM 33004 SG CYS w 17 75.528 52.443 55.865 1.00161.53 S ATOM 33028 SG CYS w 20 78.925 53.543 57.363 1.00163.91 S ATOM 33189 SG CYS w 39 76.702 56.215 56.469 1.00169.29 S ATOM 33214 SG CYS w 42 78.026 54.003 53.672 1.00167.79 S ATOM 33566 SG CYS w 86 44.242 43.145 86.133 1.00150.39 S ATOM 33590 SG CYS w 89 44.838 39.685 87.838 1.00155.57 S ATOM 33794 SG CYS w 114 46.534 42.875 89.131 1.00146.35 S ATOM 33829 SG CYS w 119 47.364 41.294 85.701 1.00152.45 S ATOM 33939 SG CYS x 7 65.574 72.293 151.588 1.00 98.61 S ATOM 33963 SG CYS x 10 63.943 73.313 154.828 1.00 95.35 S ATOM 34227 SG CYS x 44 61.738 72.487 151.640 1.00107.46 S ATOM 34233 SG CYS x 45 63.284 70.107 154.080 1.00108.23 S ATOM 35379 SG CYS z 19 107.111 61.297 142.288 1.00146.64 S ATOM 35398 SG CYS z 22 107.948 58.761 144.868 1.00145.85 S ATOM 35515 SG CYS z 36 110.683 61.313 143.948 1.00153.01 S ATOM 35541 SG CYS z 39 109.452 58.949 141.263 1.00150.68 S Time building chain proxies: 18.42, per 1000 atoms: 0.52 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 6959 8.00 N 6278 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.84 Conformation dependent library (CDL) restraints added in 6.2 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 p1137 " pdb="ZN ZN p1202 " - pdb=" SG CYS p1122 " 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 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 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 19 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 39 " 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: 141 helices and 42 sheets defined 32.5% alpha, 14.8% beta 34 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 14.66 Creating SS restraints... Processing helix chain 'S' and resid 6 through 8 No H-bonds generated for 'chain 'S' and resid 6 through 8' Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 157 through 165 Processing helix chain 'S' and resid 173 through 179 Processing helix chain 'T' and resid 10 through 14 Processing helix chain 'T' and resid 25 through 34 removed outlier: 4.170A pdb=" N ALA T 34 " --> pdb=" O GLN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 63 No H-bonds generated for 'chain 'T' and resid 60 through 63' Processing helix chain 'o' and resid 28 through 34 Processing helix chain 'o' and resid 99 through 109 Processing helix chain 'o' and resid 124 through 132 Processing helix chain 'o' and resid 137 through 150 removed outlier: 4.209A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.849A 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: 3.628A 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: 4.132A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 539 through 548 removed outlier: 3.586A pdb=" N LYS o 547 " --> pdb=" O ALA o 544 " (cutoff:3.500A) Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.831A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.936A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.196A 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: 4.421A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU o 856 " --> pdb=" O VAL o 852 " (cutoff:3.500A) Processing helix chain 'o' and resid 891 through 893 No H-bonds generated for 'chain 'o' and resid 891 through 893' Processing helix chain 'o' and resid 913 through 920 Processing helix chain 'o' and resid 927 through 933 Processing helix chain 'o' and resid 936 through 944 Processing helix chain 'o' and resid 946 through 969 Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1018 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.101A 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: 3.759A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.055A 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: 3.792A 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: 3.910A pdb=" N TRP p 27 " --> pdb=" O GLN p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 61 Processing helix chain 'p' and resid 110 through 115 Processing helix chain 'p' and resid 168 through 173 Processing helix chain 'p' and resid 247 through 252 Processing helix chain 'p' and resid 269 through 275 Processing helix chain 'p' and resid 281 through 288 Processing helix chain 'p' and resid 295 through 307 Proline residue: p 303 - end of helix Processing helix chain 'p' and resid 314 through 323 Processing helix chain 'p' and resid 332 through 345 Processing helix chain 'p' and resid 358 through 377 Processing helix chain 'p' and resid 388 through 390 No H-bonds generated for 'chain 'p' and resid 388 through 390' Processing helix chain 'p' and resid 396 through 425 Processing helix chain 'p' and resid 431 through 434 No H-bonds generated for 'chain 'p' and resid 431 through 434' Processing helix chain 'p' and resid 437 through 450 Processing helix chain 'p' and resid 475 through 482 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 539 through 548 Processing helix chain 'p' and resid 580 through 593 Processing helix chain 'p' and resid 637 through 644 Processing helix chain 'p' and resid 653 through 658 Processing helix chain 'p' and resid 667 through 672 removed outlier: 3.782A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) Processing helix chain 'p' and resid 679 through 682 No H-bonds generated for 'chain 'p' and resid 679 through 682' Processing helix chain 'p' and resid 700 through 703 Processing helix chain 'p' and resid 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: 3.722A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 762 through 767 Processing helix chain 'p' and resid 798 through 803 Processing helix chain 'p' and resid 969 through 975 Proline residue: p 973 - end of helix Processing helix chain 'p' and resid 978 through 993 Processing helix chain 'p' and resid 1008 through 1018 removed outlier: 3.557A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.847A 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: 4.075A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.652A pdb=" N VAL q 245 " --> pdb=" O PRO q 241 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 27 No H-bonds generated for 'chain 'r' and resid 24 through 27' Processing helix chain 'r' and resid 34 through 50 Processing helix chain 'r' and resid 59 through 70 Processing helix chain 'r' and resid 77 through 89 Processing helix chain 'r' and resid 94 through 103 Processing helix chain 'r' and resid 108 through 114 Processing helix chain 'r' and resid 116 through 118 No H-bonds generated for 'chain 'r' and resid 116 through 118' Processing helix chain 'r' and resid 124 through 137 Processing helix chain 's' and resid 3 through 23 Processing helix chain 's' and resid 30 through 33 No H-bonds generated for 'chain 's' and resid 30 through 33' Processing helix chain 's' and resid 37 through 44 Processing helix chain 's' and resid 84 through 97 Processing helix chain 's' and resid 112 through 120 Processing helix chain 's' and resid 132 through 136 Processing helix chain 's' and resid 139 through 141 No H-bonds generated for 'chain 's' and resid 139 through 141' Processing helix chain 's' and resid 153 through 162 Processing helix chain 's' and resid 178 through 183 Processing helix chain 't' and resid 59 through 75 Processing helix chain 't' and resid 89 through 99 Processing helix chain 'u' and resid 15 through 17 No H-bonds generated for 'chain 'u' and resid 15 through 17' Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'w' and resid 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: 4.061A pdb=" N TRP x 18 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU x 19 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA x 20 " --> pdb=" O LYS x 17 " (cutoff:3.500A) Processing helix chain 'x' and resid 31 through 37 Processing helix chain 'x' and resid 43 through 50 removed outlier: 3.602A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.711A 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: 3.789A 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: 6.825A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.009A 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: 3.582A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.282A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.687A 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: 3.606A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.398A 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: 4.639A 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: 3.583A 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: 6.102A 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: 3.967A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.108A 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: 3.546A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.147A 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: 4.349A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.608A 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: 3.722A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.217A 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: 6.849A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'p' and resid 530 through 532 Processing sheet with id= W, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.555A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL p 904 " --> pdb=" O ARG p 924 " (cutoff:3.500A) Processing sheet with id= X, 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: 6.193A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'p' and resid 827 through 829 Processing sheet with id= Z, first strand: chain 'p' and resid 1113 through 1119 Processing sheet with id= AA, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id= AB, first strand: chain 'q' and resid 182 through 185 removed outlier: 6.843A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL q 9 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 98 through 106 removed outlier: 6.078A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE q 45 " --> pdb=" O GLY q 168 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 113 through 116 Processing sheet with id= AE, first strand: chain 's' and resid 60 through 62 removed outlier: 6.278A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 's' and resid 147 through 150 removed outlier: 3.701A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 't' and resid 105 through 109 Processing sheet with id= AH, first strand: chain 'u' and resid 2 through 13 removed outlier: 3.556A pdb=" N ALA u 47 " --> pdb=" O ILE u 75 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE u 77 " --> pdb=" O VAL u 45 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL u 45 " --> pdb=" O PHE u 77 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'u' and resid 142 through 146 removed outlier: 7.006A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.147A 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: 4.751A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE u 147 " --> pdb=" O SER u 162 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'u' and resid 127 through 129 Processing sheet with id= AK, first strand: chain 'u' and resid 50 through 54 removed outlier: 6.852A pdb=" N LYS u 71 " --> pdb=" O ASP u 52 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'v' and resid 25 through 31 removed outlier: 5.312A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'w' and resid 24 through 28 Processing sheet with id= AN, first strand: chain 'w' and resid 79 through 81 Processing sheet with id= AO, first strand: chain 'y' and resid 19 through 23 Processing sheet with id= AP, first strand: chain 'z' and resid 16 through 18 1145 hydrogen bonds defined for protein. 3201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 19.87 Time building geometry restraints manager: 15.73 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: 9444 1.33 - 1.49: 12000 1.49 - 1.65: 14863 1.65 - 1.82: 325 Bond restraints: 36655 Sorted by residual: bond pdb=" C4' G2L Z 17 " pdb=" C3' G2L Z 17 " ideal model delta sigma weight residual 1.270 1.521 -0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C2' G2L Z 17 " pdb=" C1' G2L Z 17 " ideal model delta sigma weight residual 1.271 1.520 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" ND2 ASN N 7 " pdb="HD22 ASN N 7 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+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 bond pdb=" N GLY N 3 " pdb=" H GLY N 3 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 ... (remaining 36650 not shown) Histogram of bond angle deviations from ideal: 75.35 - 88.72: 1 88.72 - 102.09: 274 102.09 - 115.46: 24129 115.46 - 128.84: 25315 128.84 - 142.21: 297 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 75.35 34.83 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 110.46 136.31 -25.85 3.00e+00 1.11e-01 7.42e+01 angle pdb=" P26 W0F p1201 " pdb=" O29 W0F p1201 " pdb=" P30 W0F p1201 " ideal model delta sigma weight residual 123.60 142.21 -18.61 3.00e+00 1.11e-01 3.85e+01 angle pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" C10 W0F p1201 " ideal model delta sigma weight residual 99.38 117.53 -18.15 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C ASP s 46 " pdb=" CA ASP s 46 " pdb=" CB ASP s 46 " ideal model delta sigma weight residual 117.23 109.68 7.55 1.36e+00 5.41e-01 3.08e+01 ... (remaining 50011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.48: 21122 31.48 - 62.96: 986 62.96 - 94.45: 37 94.45 - 125.93: 2 125.93 - 157.41: 1 Dihedral angle restraints: 22148 sinusoidal: 9988 harmonic: 12160 Sorted by residual: dihedral pdb=" O4' U Z 7 " pdb=" C1' U Z 7 " pdb=" N1 U Z 7 " pdb=" C2 U Z 7 " ideal model delta sinusoidal sigma weight residual 200.00 42.59 157.41 1 1.50e+01 4.44e-03 8.21e+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 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA PRO w 117 " pdb=" C PRO w 117 " pdb=" N HIS w 118 " pdb=" CA HIS w 118 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 22145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4953 0.074 - 0.149: 599 0.149 - 0.223: 12 0.223 - 0.297: 1 0.297 - 0.372: 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 3.46e+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 3.07e+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 2.64e+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 4.15e-02 5.17e+01 pdb=" C10 W0F p1201 " 0.041 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 " -0.017 2.00e-02 2.50e+03 pdb=" N19 W0F p1201 " 0.006 2.00e-02 2.50e+03 pdb=" O18 W0F p1201 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.022 2.00e-02 2.50e+03 4.47e-02 1.99e+01 pdb=" C ILE p 51 " 0.077 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE p 50 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PHE p 50 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE p 50 " -0.027 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 - 2.40: 47 2.40 - 2.95: 16075 2.95 - 3.50: 41488 3.50 - 4.05: 70731 4.05 - 4.60: 101861 Nonbonded interactions: 230202 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.845 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 1.897 2.050 nonbonded pdb="HG22 ILE N 4 " pdb="HD13 ILE N 4 " model vdw 2.020 2.440 nonbonded pdb=" OD2 ASP o 497 " pdb=" O33 W0F p1201 " model vdw 2.035 2.800 ... (remaining 230197 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: 1.650 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: 0.830 Extract box with map and model: 8.460 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 112.030 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5365 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 : 0.007 0.251 36632 Z= 0.428 Angle : 0.735 34.827 49964 Z= 0.378 Chirality : 0.046 0.372 5568 Planarity : 0.004 0.074 6099 Dihedral : 15.568 157.410 14275 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.99 % Favored : 95.82 % Rotamer: Outliers : 1.17 % Allowed : 5.97 % Favored : 92.87 % 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: 0.50 (0.13), residues: 4137 helix: 1.33 (0.14), residues: 1418 sheet: 0.22 (0.20), residues: 661 loop : -0.27 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP o1192 HIS 0.007 0.001 HIS p 842 PHE 0.017 0.002 PHE q 93 TYR 0.036 0.002 TYR o 669 ARG 0.010 0.001 ARG p 472 *********************** 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 988 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 945 time to evaluate : 4.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 18 ILE cc_start: 0.7938 (mt) cc_final: 0.7711 (mm) REVERT: o 19 LYS cc_start: 0.7535 (mttp) cc_final: 0.7174 (mmmt) REVERT: o 58 MET cc_start: 0.8015 (ttp) cc_final: 0.7701 (ttm) REVERT: o 67 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8420 (tpm170) REVERT: o 103 THR cc_start: 0.7661 (m) cc_final: 0.7402 (p) REVERT: o 136 GLN cc_start: 0.6546 (mp10) cc_final: 0.6209 (mp10) REVERT: o 138 LYS cc_start: 0.7091 (tttm) cc_final: 0.6750 (ttpt) REVERT: o 271 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7595 (ptp-110) REVERT: o 355 MET cc_start: 0.8622 (mmm) cc_final: 0.8194 (mmm) REVERT: o 382 ARG cc_start: 0.6313 (mtp-110) cc_final: 0.5770 (ttm110) REVERT: o 451 CYS cc_start: 0.6515 (m) cc_final: 0.6063 (p) REVERT: o 470 MET cc_start: 0.8603 (mtm) cc_final: 0.8265 (mtp) REVERT: o 495 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5786 (p0) REVERT: o 524 MET cc_start: 0.7683 (mmp) cc_final: 0.7392 (mmm) REVERT: o 538 VAL cc_start: 0.8481 (p) cc_final: 0.8230 (m) REVERT: o 559 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7352 (mt-10) REVERT: o 587 THR cc_start: 0.7944 (m) cc_final: 0.7699 (p) REVERT: o 612 ASP cc_start: 0.7180 (m-30) cc_final: 0.6506 (p0) REVERT: o 653 VAL cc_start: 0.7291 (t) cc_final: 0.7028 (m) REVERT: o 700 GLN cc_start: 0.6776 (tt0) cc_final: 0.5928 (tp40) REVERT: o 711 GLN cc_start: 0.5996 (tt0) cc_final: 0.5795 (mm-40) REVERT: o 715 GLU cc_start: 0.6339 (mt-10) cc_final: 0.6015 (mm-30) REVERT: o 796 LYS cc_start: 0.6789 (mttt) cc_final: 0.6505 (mttp) REVERT: o 811 ILE cc_start: 0.7445 (mt) cc_final: 0.7047 (pt) REVERT: o 818 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7506 (mm-30) REVERT: o 868 MET cc_start: 0.7911 (ptt) cc_final: 0.7558 (ptm) REVERT: o 905 ASN cc_start: 0.7029 (m-40) cc_final: 0.6778 (t0) REVERT: o 919 LYS cc_start: 0.6849 (mttt) cc_final: 0.6532 (mmtm) REVERT: o 953 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7379 (mt-10) REVERT: o 1071 GLU cc_start: 0.6402 (tp30) cc_final: 0.6070 (tp30) REVERT: o 1132 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7603 (mtmm) REVERT: o 1133 LYS cc_start: 0.7666 (mttt) cc_final: 0.7459 (mtmp) REVERT: o 1135 LYS cc_start: 0.8280 (mttt) cc_final: 0.7968 (ttmp) REVERT: o 1136 THR cc_start: 0.8538 (m) cc_final: 0.8199 (p) REVERT: o 1167 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7265 (ttm-80) REVERT: o 1220 HIS cc_start: 0.6773 (m-70) cc_final: 0.6450 (m-70) REVERT: o 1284 PHE cc_start: 0.7914 (t80) cc_final: 0.7584 (t80) REVERT: o 1302 GLU cc_start: 0.7949 (pt0) cc_final: 0.7432 (mp0) REVERT: o 1303 GLN cc_start: 0.8415 (mt0) cc_final: 0.8181 (mp10) REVERT: o 1306 LYS cc_start: 0.6925 (mttt) cc_final: 0.6042 (tttp) REVERT: o 1337 GLU cc_start: 0.6210 (mt-10) cc_final: 0.5992 (mt-10) REVERT: o 1339 ASP cc_start: 0.7078 (t0) cc_final: 0.6466 (m-30) REVERT: o 1364 GLU cc_start: 0.6657 (tp30) cc_final: 0.6381 (tp30) REVERT: o 1383 TYR cc_start: 0.6765 (t80) cc_final: 0.6361 (t80) REVERT: o 1391 SER cc_start: 0.6992 (t) cc_final: 0.6576 (p) REVERT: o 1414 ILE cc_start: 0.8138 (mm) cc_final: 0.7510 (mp) REVERT: o 1422 GLN cc_start: 0.7018 (mt0) cc_final: 0.6294 (mm110) REVERT: o 1428 MET cc_start: 0.6952 (ttm) cc_final: 0.6748 (ttm) REVERT: o 1437 ASP cc_start: 0.6684 (m-30) cc_final: 0.6479 (t0) REVERT: o 1441 GLU cc_start: 0.5274 (tp30) cc_final: 0.4974 (tt0) REVERT: o 1462 GLN cc_start: 0.6599 (mt0) cc_final: 0.6371 (mt0) REVERT: o 1476 ASP cc_start: 0.5308 (t0) cc_final: 0.4580 (t0) REVERT: p 21 LEU cc_start: 0.7031 (tp) cc_final: 0.6641 (tt) REVERT: p 23 GLN cc_start: 0.7188 (mm-40) cc_final: 0.6823 (tp40) REVERT: p 98 HIS cc_start: 0.6634 (t70) cc_final: 0.6387 (t-170) REVERT: p 109 MET cc_start: 0.7427 (mmm) cc_final: 0.7189 (mmt) REVERT: p 141 GLN cc_start: 0.8256 (pt0) cc_final: 0.7834 (pp30) REVERT: p 143 GLN cc_start: 0.7273 (pt0) cc_final: 0.6595 (pm20) REVERT: p 200 MET cc_start: 0.7714 (ttm) cc_final: 0.7352 (ttp) REVERT: p 208 PHE cc_start: 0.7419 (m-80) cc_final: 0.7200 (m-80) REVERT: p 239 MET cc_start: 0.7227 (ttm) cc_final: 0.6955 (ttm) REVERT: p 254 GLN cc_start: 0.7196 (mt0) cc_final: 0.6594 (pm20) REVERT: p 266 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7684 (mt-10) REVERT: p 281 ASP cc_start: 0.6084 (m-30) cc_final: 0.5740 (m-30) REVERT: p 299 GLU cc_start: 0.7297 (tp30) cc_final: 0.6660 (tm-30) REVERT: p 309 PHE cc_start: 0.8669 (t80) cc_final: 0.8430 (t80) REVERT: p 320 PHE cc_start: 0.8404 (t80) cc_final: 0.7991 (t80) REVERT: p 324 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7532 (mtm-85) REVERT: p 381 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7902 (mt-10) REVERT: p 386 ASP cc_start: 0.6901 (m-30) cc_final: 0.6115 (t0) REVERT: p 394 ASP cc_start: 0.7248 (m-30) cc_final: 0.6901 (m-30) REVERT: p 432 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6840 (mp0) REVERT: p 439 ILE cc_start: 0.7463 (mt) cc_final: 0.7248 (mt) REVERT: p 442 ASP cc_start: 0.6293 (m-30) cc_final: 0.5947 (m-30) REVERT: p 471 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7486 (t0) REVERT: p 477 SER cc_start: 0.7663 (t) cc_final: 0.7413 (p) REVERT: p 522 LEU cc_start: 0.7985 (mt) cc_final: 0.7328 (mt) REVERT: p 546 GLU cc_start: 0.6063 (mt-10) cc_final: 0.5805 (mt-10) REVERT: p 574 VAL cc_start: 0.7029 (t) cc_final: 0.6273 (t) REVERT: p 606 ASP cc_start: 0.5460 (t0) cc_final: 0.5059 (p0) REVERT: p 610 ARG cc_start: 0.5753 (mtt90) cc_final: 0.5430 (mtm-85) REVERT: p 611 GLU cc_start: 0.6406 (mm-30) cc_final: 0.5710 (mt-10) REVERT: p 674 MET cc_start: 0.7942 (mmm) cc_final: 0.7259 (mmm) REVERT: p 710 ILE cc_start: 0.7663 (pt) cc_final: 0.7374 (mp) REVERT: p 728 MET cc_start: 0.7098 (mtm) cc_final: 0.6418 (mtp) REVERT: p 737 ILE cc_start: 0.8044 (mt) cc_final: 0.7480 (tp) REVERT: p 796 MET cc_start: 0.8390 (mtm) cc_final: 0.7849 (mtm) REVERT: p 817 GLN cc_start: 0.7060 (tt0) cc_final: 0.6658 (pm20) REVERT: p 827 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6551 (mt-10) REVERT: p 906 GLN cc_start: 0.7842 (tt0) cc_final: 0.7438 (tp-100) REVERT: p 959 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7219 (mt-10) REVERT: p 1022 LEU cc_start: 0.7324 (mt) cc_final: 0.6991 (mt) REVERT: p 1054 MET cc_start: 0.7879 (mtm) cc_final: 0.7581 (mtt) REVERT: p 1076 GLU cc_start: 0.7384 (tt0) cc_final: 0.6932 (tt0) REVERT: p 1080 ARG cc_start: 0.6657 (mtt90) cc_final: 0.6357 (mtm-85) REVERT: p 1121 LEU cc_start: 0.7919 (mt) cc_final: 0.7700 (mt) REVERT: p 1151 MET cc_start: 0.7780 (ptm) cc_final: 0.7464 (ptm) REVERT: p 1165 MET cc_start: 0.6927 (mtm) cc_final: 0.6329 (mtp) REVERT: p 1172 MET cc_start: 0.7448 (mmt) cc_final: 0.7142 (mmt) REVERT: q 17 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7070 (pm20) REVERT: q 51 GLN cc_start: 0.7745 (tt0) cc_final: 0.7062 (tt0) REVERT: q 61 ASP cc_start: 0.8142 (m-30) cc_final: 0.7832 (m-30) REVERT: q 108 ASN cc_start: 0.7092 (m-40) cc_final: 0.5648 (m-40) REVERT: q 109 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6891 (pm20) REVERT: q 111 GLN cc_start: 0.7668 (tt0) cc_final: 0.7366 (mp10) REVERT: q 186 TYR cc_start: 0.8164 (p90) cc_final: 0.7936 (p90) REVERT: q 199 LYS cc_start: 0.7791 (mttt) cc_final: 0.7443 (mtmm) REVERT: q 202 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7536 (mt-10) REVERT: q 220 TYR cc_start: 0.7626 (t80) cc_final: 0.7411 (t80) REVERT: q 225 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8393 (ptmm) REVERT: q 234 GLU cc_start: 0.7550 (tt0) cc_final: 0.6472 (mm-30) REVERT: q 236 CYS cc_start: 0.7544 (t) cc_final: 0.7148 (t) REVERT: s 49 SER cc_start: 0.8462 (t) cc_final: 0.7554 (p) REVERT: s 84 ILE cc_start: 0.7668 (mt) cc_final: 0.7250 (tp) REVERT: s 91 CYS cc_start: 0.8945 (t) cc_final: 0.8657 (t) REVERT: s 133 GLN cc_start: 0.7656 (mt0) cc_final: 0.7226 (mp10) REVERT: s 197 SER cc_start: 0.8779 (t) cc_final: 0.8541 (p) REVERT: t 57 MET cc_start: 0.7324 (ttp) cc_final: 0.7047 (ttm) REVERT: t 79 VAL cc_start: 0.7645 (t) cc_final: 0.6848 (p) REVERT: t 80 MET cc_start: 0.7599 (mmt) cc_final: 0.6103 (mmt) REVERT: t 82 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7728 (tm-30) REVERT: t 86 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6028 (mt-10) REVERT: t 116 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6988 (tt0) REVERT: u 10 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7912 (mt-10) REVERT: u 68 TYR cc_start: 0.5853 (m-80) cc_final: 0.5570 (m-80) REVERT: u 157 ILE cc_start: 0.6419 (mt) cc_final: 0.5266 (mt) REVERT: u 158 PHE cc_start: 0.5599 (p90) cc_final: 0.2418 (p90) REVERT: v 37 MET cc_start: 0.7443 (mtp) cc_final: 0.6803 (mtt) REVERT: v 63 THR cc_start: 0.8449 (p) cc_final: 0.8081 (t) REVERT: v 90 TYR cc_start: 0.8490 (t80) cc_final: 0.8069 (t80) REVERT: v 100 GLU cc_start: 0.7186 (tt0) cc_final: 0.6215 (mt-10) REVERT: v 102 ASP cc_start: 0.8066 (t0) cc_final: 0.7855 (t0) REVERT: v 105 SER cc_start: 0.8239 (t) cc_final: 0.7672 (p) REVERT: v 136 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7523 (mt-10) REVERT: w 28 GLU cc_start: 0.6672 (tt0) cc_final: 0.6266 (pt0) REVERT: w 56 ASN cc_start: 0.7728 (t0) cc_final: 0.7250 (t0) REVERT: w 71 ASP cc_start: 0.7086 (m-30) cc_final: 0.6524 (m-30) REVERT: w 93 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7313 (mm-30) REVERT: x 12 LYS cc_start: 0.7237 (ttmt) cc_final: 0.6805 (ttmm) REVERT: x 57 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7716 (mm-30) REVERT: y 2 ASN cc_start: 0.8480 (m-40) cc_final: 0.8047 (m110) REVERT: y 7 PHE cc_start: 0.6812 (p90) cc_final: 0.6290 (p90) REVERT: y 8 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7076 (mp0) REVERT: y 23 LYS cc_start: 0.7733 (mttt) cc_final: 0.7241 (mptt) REVERT: z 41 TYR cc_start: 0.7675 (t80) cc_final: 0.7466 (t80) outliers start: 43 outliers final: 7 residues processed: 974 average time/residue: 1.6613 time to fit residues: 1907.0659 Evaluate side-chains 581 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 572 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 675 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 1004 ASP Chi-restraints excluded: chain q residue 44 ILE 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: 1.9990 chunk 109 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 329 optimal weight: 50.0000 chunk 127 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 245 optimal weight: 0.7980 chunk 382 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 178 GLN o 62 GLN o 143 HIS o 181 HIS o 296 ASN ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN o 531 ASN o 539 GLN o 671 ASN o 765 ASN o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN o 935 GLN o1024 ASN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1384 HIS o1462 GLN p 43 GLN p 111 ASN p 245 GLN ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 639 HIS ** p 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 699 HIS p 718 GLN ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 838 GLN p 941 GLN p 948 GLN p1007 ASN p1021 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN r 66 ASN r 129 GLN s 64 HIS s 107 GLN t 46 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN w 22 ASN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 74 GLN w 98 GLN w 118 HIS z 23 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5489 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 36632 Z= 0.346 Angle : 0.574 10.610 49964 Z= 0.304 Chirality : 0.043 0.178 5568 Planarity : 0.004 0.049 6099 Dihedral : 17.230 155.208 5835 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 25.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.96 % Favored : 95.87 % Rotamer: Outliers : 4.28 % Allowed : 14.21 % Favored : 81.51 % 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: 0.57 (0.13), residues: 4137 helix: 1.51 (0.14), residues: 1391 sheet: -0.02 (0.19), residues: 672 loop : -0.19 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP o 479 HIS 0.011 0.002 HIS r 43 PHE 0.025 0.002 PHE o 397 TYR 0.022 0.002 TYR o 669 ARG 0.009 0.001 ARG p 975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 589 time to evaluate : 3.886 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: S 170 VAL cc_start: 0.5493 (OUTLIER) cc_final: 0.4897 (t) REVERT: o 19 LYS cc_start: 0.7374 (mttp) cc_final: 0.6966 (mmmt) REVERT: o 33 ARG cc_start: 0.6854 (mtm110) cc_final: 0.6614 (mtm-85) REVERT: o 58 MET cc_start: 0.8204 (ttp) cc_final: 0.7831 (ttm) REVERT: o 67 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8439 (tpm170) REVERT: o 118 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7570 (mp) REVERT: o 120 ASP cc_start: 0.6986 (m-30) cc_final: 0.6598 (t0) REVERT: o 138 LYS cc_start: 0.7085 (tttm) cc_final: 0.6762 (ttpt) REVERT: o 327 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6348 (mmt-90) REVERT: o 336 LEU cc_start: 0.7334 (mt) cc_final: 0.7045 (mm) REVERT: o 355 MET cc_start: 0.8492 (mmm) cc_final: 0.8079 (mmm) REVERT: o 451 CYS cc_start: 0.6387 (m) cc_final: 0.5772 (p) REVERT: o 470 MET cc_start: 0.8674 (mtm) cc_final: 0.8165 (mtp) REVERT: o 532 ARG cc_start: 0.6253 (mtm110) cc_final: 0.5398 (ptp90) REVERT: o 538 VAL cc_start: 0.8525 (p) cc_final: 0.8297 (m) REVERT: o 556 GLU cc_start: 0.6954 (tp30) cc_final: 0.6247 (mt-10) REVERT: o 612 ASP cc_start: 0.7324 (m-30) cc_final: 0.6581 (p0) REVERT: o 659 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.5821 (mp0) REVERT: o 700 GLN cc_start: 0.6894 (tt0) cc_final: 0.6042 (tp40) REVERT: o 711 GLN cc_start: 0.6069 (tt0) cc_final: 0.5788 (mm-40) REVERT: o 715 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5881 (mm-30) REVERT: o 761 SER cc_start: 0.7633 (m) cc_final: 0.7303 (t) REVERT: o 796 LYS cc_start: 0.6900 (mttt) cc_final: 0.6576 (mttp) REVERT: o 818 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7315 (mm-30) REVERT: o 868 MET cc_start: 0.7906 (ptt) cc_final: 0.7648 (ptm) REVERT: o 872 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8125 (ttm) REVERT: o 905 ASN cc_start: 0.7576 (m-40) cc_final: 0.7347 (m-40) REVERT: o 1056 GLU cc_start: 0.6306 (mt-10) cc_final: 0.6091 (pt0) REVERT: o 1085 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6813 (mt-10) REVERT: o 1132 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7774 (mtmm) REVERT: o 1167 ARG cc_start: 0.8103 (ttp-110) cc_final: 0.7584 (ttm-80) REVERT: o 1196 TYR cc_start: 0.6889 (m-80) cc_final: 0.6633 (m-80) REVERT: o 1219 LYS cc_start: 0.8353 (tptt) cc_final: 0.7733 (tptt) REVERT: o 1262 MET cc_start: 0.7221 (ttt) cc_final: 0.6551 (ttm) REVERT: o 1279 MET cc_start: 0.6789 (mmp) cc_final: 0.6406 (mpp) REVERT: o 1282 ASP cc_start: 0.7454 (p0) cc_final: 0.7185 (p0) REVERT: o 1302 GLU cc_start: 0.8136 (pt0) cc_final: 0.7502 (mp0) REVERT: o 1303 GLN cc_start: 0.8378 (mt0) cc_final: 0.8087 (mp10) REVERT: o 1306 LYS cc_start: 0.6548 (mttt) cc_final: 0.5868 (tttp) REVERT: o 1339 ASP cc_start: 0.6777 (t0) cc_final: 0.6187 (m-30) REVERT: o 1341 VAL cc_start: 0.8596 (p) cc_final: 0.8095 (t) REVERT: o 1350 LYS cc_start: 0.6941 (tttm) cc_final: 0.6379 (mptt) REVERT: o 1351 ASP cc_start: 0.6797 (m-30) cc_final: 0.6416 (m-30) REVERT: o 1364 GLU cc_start: 0.6944 (tp30) cc_final: 0.6345 (tp30) REVERT: o 1383 TYR cc_start: 0.6514 (t80) cc_final: 0.6088 (t80) REVERT: o 1391 SER cc_start: 0.7218 (t) cc_final: 0.6748 (p) REVERT: o 1412 MET cc_start: 0.7946 (ttp) cc_final: 0.7605 (ttm) REVERT: o 1422 GLN cc_start: 0.7112 (mt0) cc_final: 0.6272 (mm110) REVERT: o 1428 MET cc_start: 0.6940 (ttm) cc_final: 0.6639 (ttm) REVERT: o 1441 GLU cc_start: 0.5353 (tp30) cc_final: 0.5094 (tt0) REVERT: o 1462 GLN cc_start: 0.7130 (mt0) cc_final: 0.6738 (mt0) REVERT: o 1476 ASP cc_start: 0.5019 (t0) cc_final: 0.4560 (t0) REVERT: p 21 LEU cc_start: 0.7071 (tp) cc_final: 0.6818 (tt) REVERT: p 23 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6922 (tp40) REVERT: p 109 MET cc_start: 0.7015 (mmm) cc_final: 0.6737 (mmt) REVERT: p 127 ASP cc_start: 0.6640 (m-30) cc_final: 0.6172 (m-30) REVERT: p 141 GLN cc_start: 0.8307 (pt0) cc_final: 0.7857 (pp30) REVERT: p 143 GLN cc_start: 0.7219 (pt0) cc_final: 0.6917 (pm20) REVERT: p 200 MET cc_start: 0.7816 (ttm) cc_final: 0.6573 (tpp) REVERT: p 239 MET cc_start: 0.7256 (ttm) cc_final: 0.6821 (ttm) REVERT: p 254 GLN cc_start: 0.7248 (mt0) cc_final: 0.6998 (pm20) REVERT: p 255 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5592 (ttp80) REVERT: p 266 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7597 (mt-10) REVERT: p 291 ASP cc_start: 0.7269 (t0) cc_final: 0.6984 (t0) REVERT: p 299 GLU cc_start: 0.7263 (tp30) cc_final: 0.6492 (tm-30) REVERT: p 309 PHE cc_start: 0.8863 (t80) cc_final: 0.8612 (t80) REVERT: p 324 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7584 (mtt90) REVERT: p 381 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7927 (mt-10) REVERT: p 386 ASP cc_start: 0.6839 (m-30) cc_final: 0.6083 (t70) REVERT: p 394 ASP cc_start: 0.7167 (m-30) cc_final: 0.6827 (m-30) REVERT: p 416 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5600 (ttm110) REVERT: p 442 ASP cc_start: 0.6359 (m-30) cc_final: 0.6035 (m-30) REVERT: p 477 SER cc_start: 0.7833 (t) cc_final: 0.7614 (p) REVERT: p 520 VAL cc_start: 0.7463 (t) cc_final: 0.7242 (p) REVERT: p 522 LEU cc_start: 0.8056 (mt) cc_final: 0.7483 (mt) REVERT: p 546 GLU cc_start: 0.6025 (mt-10) cc_final: 0.5765 (mt-10) REVERT: p 548 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.6333 (m-90) REVERT: p 606 ASP cc_start: 0.5742 (t0) cc_final: 0.4484 (p0) REVERT: p 610 ARG cc_start: 0.6383 (mtt90) cc_final: 0.5806 (mtm-85) REVERT: p 611 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6178 (mt-10) REVERT: p 728 MET cc_start: 0.7073 (mtm) cc_final: 0.6344 (mtp) REVERT: p 737 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7697 (mm) REVERT: p 796 MET cc_start: 0.8671 (mtm) cc_final: 0.7979 (mtm) REVERT: p 817 GLN cc_start: 0.7320 (tt0) cc_final: 0.6894 (pm20) REVERT: p 827 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6492 (mt-10) REVERT: p 850 ASP cc_start: 0.7926 (t0) cc_final: 0.7672 (t0) REVERT: p 863 ASP cc_start: 0.7476 (m-30) cc_final: 0.6961 (t70) REVERT: p 897 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5169 (mpt-90) REVERT: p 906 GLN cc_start: 0.8017 (tt0) cc_final: 0.7519 (mm-40) REVERT: p 959 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7582 (mt-10) REVERT: p 1054 MET cc_start: 0.8062 (mtm) cc_final: 0.7413 (mtm) REVERT: p 1076 GLU cc_start: 0.7318 (tt0) cc_final: 0.6766 (tt0) REVERT: p 1080 ARG cc_start: 0.6565 (mtt90) cc_final: 0.6137 (mtm-85) REVERT: p 1151 MET cc_start: 0.7858 (ptm) cc_final: 0.7467 (ptm) REVERT: p 1165 MET cc_start: 0.6775 (mtm) cc_final: 0.6483 (mtp) REVERT: p 1172 MET cc_start: 0.7552 (mmt) cc_final: 0.7188 (mmt) REVERT: q 6 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7864 (mm-40) REVERT: q 17 GLU cc_start: 0.7578 (mt-10) cc_final: 0.6953 (pm20) REVERT: q 61 ASP cc_start: 0.8520 (m-30) cc_final: 0.8196 (m-30) REVERT: q 109 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6843 (pm20) REVERT: q 111 GLN cc_start: 0.7792 (tt0) cc_final: 0.7465 (mp10) REVERT: q 199 LYS cc_start: 0.7857 (mttt) cc_final: 0.7640 (mtmt) REVERT: q 202 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7760 (mt-10) REVERT: s 3 ASP cc_start: 0.5877 (OUTLIER) cc_final: 0.5394 (t70) REVERT: s 9 ARG cc_start: 0.5858 (mtt180) cc_final: 0.5521 (mtt90) REVERT: s 26 TYR cc_start: 0.7576 (m-80) cc_final: 0.7255 (m-80) REVERT: s 49 SER cc_start: 0.8205 (t) cc_final: 0.7740 (p) REVERT: s 154 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6818 (mp0) REVERT: s 197 SER cc_start: 0.8637 (t) cc_final: 0.8381 (t) REVERT: t 57 MET cc_start: 0.7716 (ttp) cc_final: 0.7172 (ttm) REVERT: t 79 VAL cc_start: 0.7233 (t) cc_final: 0.6814 (p) REVERT: t 80 MET cc_start: 0.6875 (mmt) cc_final: 0.6594 (mmt) REVERT: t 81 VAL cc_start: 0.6545 (t) cc_final: 0.6137 (m) REVERT: t 82 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7958 (tm-30) REVERT: t 86 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6807 (tp30) REVERT: u 10 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7984 (mt-10) REVERT: u 16 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.5944 (ptp-170) REVERT: u 107 PHE cc_start: 0.4835 (m-80) cc_final: 0.4583 (m-80) REVERT: u 157 ILE cc_start: 0.4501 (mt) cc_final: 0.4265 (mt) REVERT: v 37 MET cc_start: 0.7705 (mtp) cc_final: 0.7182 (mtt) REVERT: v 38 ASP cc_start: 0.6035 (OUTLIER) cc_final: 0.5323 (m-30) REVERT: v 63 THR cc_start: 0.8401 (p) cc_final: 0.8086 (t) REVERT: v 95 LYS cc_start: 0.6435 (tttt) cc_final: 0.6159 (ttpt) REVERT: v 100 GLU cc_start: 0.7080 (tt0) cc_final: 0.6266 (mt-10) REVERT: v 102 ASP cc_start: 0.8290 (t0) cc_final: 0.8055 (t0) REVERT: v 103 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: v 136 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7356 (mt-10) REVERT: v 146 LYS cc_start: 0.6410 (tttt) cc_final: 0.6145 (tttp) REVERT: w 28 GLU cc_start: 0.6543 (tt0) cc_final: 0.6164 (pt0) REVERT: w 71 ASP cc_start: 0.7230 (m-30) cc_final: 0.6864 (m-30) REVERT: w 80 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6391 (ptm160) REVERT: w 93 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7406 (mm-30) REVERT: w 122 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6834 (mpp80) REVERT: x 12 LYS cc_start: 0.7102 (ttmt) cc_final: 0.6635 (ttmm) REVERT: x 19 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: x 57 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7779 (mm-30) REVERT: y 8 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7205 (mp0) REVERT: y 22 ASN cc_start: 0.6250 (m-40) cc_final: 0.5959 (m110) REVERT: y 23 LYS cc_start: 0.7842 (mttt) cc_final: 0.7369 (mptt) REVERT: y 70 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7602 (ttmm) REVERT: y 103 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6921 (tm-30) REVERT: y 110 LYS cc_start: 0.7473 (tptp) cc_final: 0.7230 (tptt) REVERT: z 16 ILE cc_start: 0.8439 (mt) cc_final: 0.8158 (mm) outliers start: 158 outliers final: 67 residues processed: 696 average time/residue: 1.5974 time to fit residues: 1348.7000 Evaluate side-chains 600 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 515 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 290 LEU Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 327 ARG Chi-restraints excluded: chain o residue 423 ASN 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 520 MET Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 632 ASN Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 647 THR Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 924 TYR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 48 ASP Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 255 ARG Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 416 ARG Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 548 TRP Chi-restraints excluded: chain p residue 589 LYS Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 737 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 849 ASP Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain r residue 38 HIS Chi-restraints excluded: chain s residue 3 ASP Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 103 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 80 ARG Chi-restraints excluded: chain w residue 122 ARG Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 318 optimal weight: 30.0000 chunk 260 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 413 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 379 optimal weight: 0.9990 chunk 130 optimal weight: 0.2980 chunk 307 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 143 HIS o 181 HIS o 296 ASN ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 330 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 485 ASN o 671 ASN o 673 GLN o 721 HIS ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 935 GLN ** o 947 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1024 ASN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1360 ASN ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN ** z 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36632 Z= 0.230 Angle : 0.483 10.853 49964 Z= 0.259 Chirality : 0.040 0.186 5568 Planarity : 0.003 0.045 6099 Dihedral : 17.017 153.173 5826 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 4.42 % Allowed : 16.16 % Favored : 79.42 % 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: 0.73 (0.13), residues: 4137 helix: 1.79 (0.14), residues: 1386 sheet: -0.04 (0.19), residues: 686 loop : -0.16 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o1192 HIS 0.018 0.001 HIS r 43 PHE 0.021 0.001 PHE o 397 TYR 0.018 0.001 TYR u 167 ARG 0.006 0.000 ARG p 975 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 541 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 19 LYS cc_start: 0.7308 (mttp) cc_final: 0.6954 (mmmt) REVERT: o 33 ARG cc_start: 0.6937 (mtm110) cc_final: 0.6683 (mtm-85) REVERT: o 45 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6239 (pm20) REVERT: o 58 MET cc_start: 0.8212 (ttp) cc_final: 0.7854 (ttm) REVERT: o 67 ARG cc_start: 0.8866 (ttp80) cc_final: 0.8413 (tpm170) REVERT: o 118 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7486 (mp) REVERT: o 120 ASP cc_start: 0.6984 (m-30) cc_final: 0.6705 (t0) REVERT: o 138 LYS cc_start: 0.7233 (tttm) cc_final: 0.6962 (ttpt) REVERT: o 227 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7858 (ptm160) REVERT: o 330 GLN cc_start: 0.5794 (OUTLIER) cc_final: 0.5507 (pm20) REVERT: o 355 MET cc_start: 0.8540 (mmm) cc_final: 0.8221 (mmm) REVERT: o 447 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7393 (mt-10) REVERT: o 451 CYS cc_start: 0.6192 (m) cc_final: 0.5678 (p) REVERT: o 470 MET cc_start: 0.8626 (mtm) cc_final: 0.8348 (mtp) REVERT: o 473 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5969 (mtm-85) REVERT: o 532 ARG cc_start: 0.6341 (mtm110) cc_final: 0.5511 (ptp90) REVERT: o 556 GLU cc_start: 0.6817 (tp30) cc_final: 0.6235 (mp0) REVERT: o 612 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6560 (p0) REVERT: o 700 GLN cc_start: 0.6903 (tt0) cc_final: 0.6051 (tp40) REVERT: o 711 GLN cc_start: 0.6089 (tt0) cc_final: 0.5735 (mm-40) REVERT: o 715 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5749 (mm-30) REVERT: o 796 LYS cc_start: 0.7190 (mttt) cc_final: 0.6876 (mttp) REVERT: o 818 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7305 (mm-30) REVERT: o 868 MET cc_start: 0.7851 (ptt) cc_final: 0.7590 (ptm) REVERT: o 872 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7984 (ttm) REVERT: o 1056 GLU cc_start: 0.6320 (mt-10) cc_final: 0.6103 (pt0) REVERT: o 1085 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6700 (mt-10) REVERT: o 1132 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7777 (mppt) REVERT: o 1167 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.7477 (ttm-80) REVERT: o 1196 TYR cc_start: 0.6817 (m-80) cc_final: 0.6614 (m-80) REVERT: o 1262 MET cc_start: 0.7294 (ttt) cc_final: 0.6975 (ttp) REVERT: o 1302 GLU cc_start: 0.8167 (pt0) cc_final: 0.7528 (mp0) REVERT: o 1303 GLN cc_start: 0.8407 (mt0) cc_final: 0.8202 (mt0) REVERT: o 1306 LYS cc_start: 0.6527 (mttt) cc_final: 0.5852 (tttp) REVERT: o 1318 LYS cc_start: 0.5811 (mtpt) cc_final: 0.5168 (mttp) REVERT: o 1334 TRP cc_start: 0.8320 (m100) cc_final: 0.7690 (m100) REVERT: o 1339 ASP cc_start: 0.6722 (t0) cc_final: 0.6195 (m-30) REVERT: o 1341 VAL cc_start: 0.8532 (p) cc_final: 0.8059 (t) REVERT: o 1350 LYS cc_start: 0.7255 (tttm) cc_final: 0.6794 (mptt) REVERT: o 1351 ASP cc_start: 0.6788 (m-30) cc_final: 0.6353 (m-30) REVERT: o 1364 GLU cc_start: 0.7079 (tp30) cc_final: 0.6442 (tp30) REVERT: o 1383 TYR cc_start: 0.6581 (t80) cc_final: 0.6131 (t80) REVERT: o 1391 SER cc_start: 0.7222 (t) cc_final: 0.6714 (p) REVERT: o 1422 GLN cc_start: 0.7032 (mt0) cc_final: 0.6412 (mm110) REVERT: o 1428 MET cc_start: 0.6668 (ttm) cc_final: 0.6377 (ttm) REVERT: o 1462 GLN cc_start: 0.7162 (mt0) cc_final: 0.6804 (mt0) REVERT: o 1484 MET cc_start: 0.2678 (ppp) cc_final: 0.2478 (ppp) REVERT: p 21 LEU cc_start: 0.6991 (tp) cc_final: 0.6731 (tt) REVERT: p 23 GLN cc_start: 0.7586 (mm-40) cc_final: 0.7246 (tp40) REVERT: p 109 MET cc_start: 0.7099 (mmm) cc_final: 0.6866 (mmt) REVERT: p 141 GLN cc_start: 0.8471 (pt0) cc_final: 0.7943 (pp30) REVERT: p 143 GLN cc_start: 0.7171 (pt0) cc_final: 0.6905 (pm20) REVERT: p 200 MET cc_start: 0.7859 (ttm) cc_final: 0.6587 (tpp) REVERT: p 239 MET cc_start: 0.7228 (ttm) cc_final: 0.6774 (ttm) REVERT: p 254 GLN cc_start: 0.7277 (mt0) cc_final: 0.7046 (pm20) REVERT: p 266 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7506 (mt-10) REVERT: p 291 ASP cc_start: 0.7242 (t0) cc_final: 0.6087 (p0) REVERT: p 299 GLU cc_start: 0.7253 (tp30) cc_final: 0.6502 (tm-30) REVERT: p 309 PHE cc_start: 0.8916 (t80) cc_final: 0.8598 (t80) REVERT: p 381 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7974 (mt-10) REVERT: p 386 ASP cc_start: 0.6776 (m-30) cc_final: 0.6094 (t70) REVERT: p 394 ASP cc_start: 0.7098 (m-30) cc_final: 0.6827 (m-30) REVERT: p 407 MET cc_start: 0.5108 (OUTLIER) cc_final: 0.4640 (mpp) REVERT: p 416 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5601 (ttm110) REVERT: p 442 ASP cc_start: 0.6265 (m-30) cc_final: 0.5949 (m-30) REVERT: p 477 SER cc_start: 0.7903 (t) cc_final: 0.7551 (p) REVERT: p 520 VAL cc_start: 0.7367 (t) cc_final: 0.7083 (p) REVERT: p 522 LEU cc_start: 0.7964 (mt) cc_final: 0.7383 (mt) REVERT: p 546 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5862 (mt-10) REVERT: p 551 GLU cc_start: 0.7255 (mp0) cc_final: 0.6679 (pm20) REVERT: p 589 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5874 (tttp) REVERT: p 728 MET cc_start: 0.6972 (mtm) cc_final: 0.6244 (mtp) REVERT: p 737 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7575 (tp) REVERT: p 786 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8173 (p) REVERT: p 796 MET cc_start: 0.8694 (mtm) cc_final: 0.8106 (mtm) REVERT: p 817 GLN cc_start: 0.7552 (tt0) cc_final: 0.6962 (pm20) REVERT: p 827 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6452 (mt-10) REVERT: p 850 ASP cc_start: 0.7958 (t0) cc_final: 0.7686 (t0) REVERT: p 863 ASP cc_start: 0.7477 (m-30) cc_final: 0.6942 (t70) REVERT: p 897 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5065 (mpt-90) REVERT: p 906 GLN cc_start: 0.8200 (tt0) cc_final: 0.7612 (mm-40) REVERT: p 959 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7585 (mt-10) REVERT: p 1054 MET cc_start: 0.8031 (mtm) cc_final: 0.7661 (mtt) REVERT: p 1076 GLU cc_start: 0.7254 (tt0) cc_final: 0.6847 (tt0) REVERT: p 1080 ARG cc_start: 0.6550 (mtt90) cc_final: 0.6132 (mtm-85) REVERT: p 1151 MET cc_start: 0.7828 (ptm) cc_final: 0.7378 (ptm) REVERT: p 1165 MET cc_start: 0.6849 (mtm) cc_final: 0.6431 (mtp) REVERT: p 1172 MET cc_start: 0.7403 (mmt) cc_final: 0.7184 (mmt) REVERT: q 6 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7865 (mm-40) REVERT: q 15 THR cc_start: 0.7541 (m) cc_final: 0.7255 (p) REVERT: q 17 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7039 (pm20) REVERT: q 74 THR cc_start: 0.8428 (m) cc_final: 0.7802 (p) REVERT: q 83 GLN cc_start: 0.7486 (mt0) cc_final: 0.7233 (mp10) REVERT: q 109 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6877 (pm20) REVERT: q 166 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.6446 (mtmt) REVERT: q 199 LYS cc_start: 0.7815 (mttt) cc_final: 0.7549 (mtmt) REVERT: q 202 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7776 (mt-10) REVERT: q 234 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: s 4 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: s 9 ARG cc_start: 0.5884 (mtt180) cc_final: 0.5642 (mtt90) REVERT: s 26 TYR cc_start: 0.7528 (m-80) cc_final: 0.6442 (m-80) REVERT: s 49 SER cc_start: 0.8210 (t) cc_final: 0.7306 (p) REVERT: s 154 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6711 (tt0) REVERT: s 167 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7119 (pt0) REVERT: s 197 SER cc_start: 0.8620 (t) cc_final: 0.8366 (t) REVERT: t 57 MET cc_start: 0.7567 (ttp) cc_final: 0.7000 (ttm) REVERT: t 79 VAL cc_start: 0.7102 (t) cc_final: 0.6739 (p) REVERT: t 80 MET cc_start: 0.6919 (mmt) cc_final: 0.6668 (mmt) REVERT: t 81 VAL cc_start: 0.6653 (t) cc_final: 0.6255 (m) REVERT: t 82 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7967 (tm-30) REVERT: t 86 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6948 (tp30) REVERT: t 116 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: u 10 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7836 (mt-10) REVERT: u 16 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.5954 (ptp-170) REVERT: v 4 ILE cc_start: 0.8408 (mt) cc_final: 0.8122 (mm) REVERT: v 37 MET cc_start: 0.7702 (mtp) cc_final: 0.7159 (mtt) REVERT: v 38 ASP cc_start: 0.6085 (OUTLIER) cc_final: 0.5391 (m-30) REVERT: v 63 THR cc_start: 0.8365 (p) cc_final: 0.8065 (t) REVERT: v 95 LYS cc_start: 0.6351 (tttt) cc_final: 0.6123 (ttpt) REVERT: v 100 GLU cc_start: 0.7063 (tt0) cc_final: 0.5924 (mt-10) REVERT: v 102 ASP cc_start: 0.8329 (t0) cc_final: 0.8073 (t0) REVERT: v 136 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7358 (mt-10) REVERT: v 146 LYS cc_start: 0.6478 (tttt) cc_final: 0.6227 (tttp) REVERT: w 28 GLU cc_start: 0.6407 (tt0) cc_final: 0.6048 (pt0) REVERT: w 71 ASP cc_start: 0.7120 (m-30) cc_final: 0.6830 (m-30) REVERT: w 93 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7549 (mm-30) REVERT: w 122 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6896 (mpp80) REVERT: x 19 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: x 57 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7792 (mm-30) REVERT: x 58 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7238 (mmtt) REVERT: y 8 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7177 (mp0) REVERT: y 22 ASN cc_start: 0.6324 (m-40) cc_final: 0.6014 (m110) REVERT: y 23 LYS cc_start: 0.7850 (mttt) cc_final: 0.7393 (mptt) REVERT: y 70 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7691 (ttmm) REVERT: y 103 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7152 (tm-30) REVERT: y 110 LYS cc_start: 0.7405 (tptp) cc_final: 0.7186 (tptp) REVERT: z 16 ILE cc_start: 0.8547 (mt) cc_final: 0.8255 (mm) outliers start: 163 outliers final: 74 residues processed: 648 average time/residue: 1.5560 time to fit residues: 1202.9137 Evaluate side-chains 599 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 502 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 227 ARG Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 330 GLN Chi-restraints excluded: chain o residue 423 ASN 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 490 THR Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 416 ARG Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 541 ILE Chi-restraints excluded: chain p residue 589 LYS Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 684 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 737 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 234 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain r residue 38 HIS Chi-restraints excluded: chain s residue 4 GLU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 116 GLU Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 120 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 54 ASP Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 122 ARG Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 384 optimal weight: 2.9990 chunk 406 optimal weight: 0.0000 chunk 200 optimal weight: 0.0050 chunk 364 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 22 GLN o 143 HIS o 181 HIS o 204 HIS o 296 ASN o 301 HIS ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 353 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN o 673 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 935 GLN o 947 HIS o1024 ASN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 486 ASN p 790 GLN ** p 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36632 Z= 0.237 Angle : 0.477 10.075 49964 Z= 0.253 Chirality : 0.040 0.175 5568 Planarity : 0.003 0.043 6099 Dihedral : 16.851 151.417 5826 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.50 % Favored : 95.36 % Rotamer: Outliers : 4.88 % Allowed : 16.32 % Favored : 78.80 % 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: 0.79 (0.13), residues: 4137 helix: 1.88 (0.14), residues: 1385 sheet: 0.03 (0.19), residues: 665 loop : -0.17 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP o1192 HIS 0.016 0.001 HIS r 43 PHE 0.020 0.001 PHE p 320 TYR 0.017 0.001 TYR v 142 ARG 0.004 0.000 ARG p1050 *********************** 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 691 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 511 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 19 LYS cc_start: 0.7218 (mttp) cc_final: 0.6850 (mmmt) REVERT: o 33 ARG cc_start: 0.6969 (mtm110) cc_final: 0.6725 (mtm-85) REVERT: o 45 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6344 (pm20) REVERT: o 67 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8406 (tpm170) REVERT: o 118 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7499 (mp) REVERT: o 120 ASP cc_start: 0.7145 (m-30) cc_final: 0.6763 (t0) REVERT: o 138 LYS cc_start: 0.7198 (tttm) cc_final: 0.6955 (ttpt) REVERT: o 327 ARG cc_start: 0.6538 (mtt-85) cc_final: 0.6020 (mmt-90) REVERT: o 336 LEU cc_start: 0.6936 (mt) cc_final: 0.6655 (mm) REVERT: o 355 MET cc_start: 0.8516 (mmm) cc_final: 0.8283 (mmm) REVERT: o 447 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7459 (mt-10) REVERT: o 451 CYS cc_start: 0.6241 (m) cc_final: 0.5705 (p) REVERT: o 470 MET cc_start: 0.8552 (mtm) cc_final: 0.8269 (mtp) REVERT: o 473 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6003 (mtm-85) REVERT: o 532 ARG cc_start: 0.6418 (mtm110) cc_final: 0.5546 (ptp90) REVERT: o 612 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6570 (p0) REVERT: o 700 GLN cc_start: 0.6890 (tt0) cc_final: 0.5961 (tp40) REVERT: o 711 GLN cc_start: 0.6098 (tt0) cc_final: 0.5773 (mm-40) REVERT: o 715 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5765 (mm-30) REVERT: o 796 LYS cc_start: 0.7203 (mttt) cc_final: 0.6877 (mttp) REVERT: o 818 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7344 (mm-30) REVERT: o 868 MET cc_start: 0.7820 (ptt) cc_final: 0.7595 (ptt) REVERT: o 872 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7982 (ttm) REVERT: o 1056 GLU cc_start: 0.6366 (mt-10) cc_final: 0.6105 (pt0) REVERT: o 1085 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6654 (mt-10) REVERT: o 1132 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7786 (mppt) REVERT: o 1167 ARG cc_start: 0.8037 (ttp-110) cc_final: 0.7491 (ttm-80) REVERT: o 1262 MET cc_start: 0.7585 (ttt) cc_final: 0.6958 (tpp) REVERT: o 1302 GLU cc_start: 0.8283 (pt0) cc_final: 0.7654 (mp0) REVERT: o 1303 GLN cc_start: 0.8435 (mt0) cc_final: 0.8196 (mt0) REVERT: o 1306 LYS cc_start: 0.6478 (mttt) cc_final: 0.5818 (tttp) REVERT: o 1318 LYS cc_start: 0.5788 (mtpt) cc_final: 0.5085 (mttp) REVERT: o 1334 TRP cc_start: 0.8262 (m100) cc_final: 0.7577 (m100) REVERT: o 1339 ASP cc_start: 0.6586 (t0) cc_final: 0.6057 (m-30) REVERT: o 1341 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8035 (t) REVERT: o 1351 ASP cc_start: 0.6760 (m-30) cc_final: 0.6154 (t0) REVERT: o 1364 GLU cc_start: 0.7054 (tp30) cc_final: 0.6432 (tp30) REVERT: o 1383 TYR cc_start: 0.6591 (t80) cc_final: 0.6124 (t80) REVERT: o 1391 SER cc_start: 0.7278 (t) cc_final: 0.6729 (p) REVERT: o 1396 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6343 (mtp85) REVERT: o 1422 GLN cc_start: 0.7052 (mt0) cc_final: 0.6575 (mm110) REVERT: o 1428 MET cc_start: 0.6698 (ttm) cc_final: 0.6397 (ttm) REVERT: o 1462 GLN cc_start: 0.7185 (mt0) cc_final: 0.6823 (mt0) REVERT: o 1484 MET cc_start: 0.2729 (ppp) cc_final: 0.2358 (ppp) REVERT: p 21 LEU cc_start: 0.7042 (tp) cc_final: 0.6744 (tt) REVERT: p 23 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7274 (tp40) REVERT: p 109 MET cc_start: 0.7055 (mmm) cc_final: 0.6815 (mmt) REVERT: p 141 GLN cc_start: 0.8497 (pt0) cc_final: 0.7944 (pp30) REVERT: p 143 GLN cc_start: 0.7129 (pt0) cc_final: 0.6906 (pm20) REVERT: p 200 MET cc_start: 0.7876 (ttm) cc_final: 0.6577 (tpp) REVERT: p 239 MET cc_start: 0.7015 (ttm) cc_final: 0.6606 (ttm) REVERT: p 254 GLN cc_start: 0.7285 (mt0) cc_final: 0.7050 (pm20) REVERT: p 266 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7535 (mt-10) REVERT: p 291 ASP cc_start: 0.7340 (t0) cc_final: 0.6134 (p0) REVERT: p 299 GLU cc_start: 0.7332 (tp30) cc_final: 0.6624 (tm-30) REVERT: p 309 PHE cc_start: 0.8907 (t80) cc_final: 0.8617 (t80) REVERT: p 318 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7091 (mp) REVERT: p 320 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7139 (t80) REVERT: p 324 ARG cc_start: 0.8291 (mtt90) cc_final: 0.7461 (mtt90) REVERT: p 381 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7988 (mt-10) REVERT: p 386 ASP cc_start: 0.6762 (m-30) cc_final: 0.6081 (t70) REVERT: p 394 ASP cc_start: 0.7141 (m-30) cc_final: 0.6868 (m-30) REVERT: p 407 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4643 (mpp) REVERT: p 416 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5612 (ttm110) REVERT: p 438 ARG cc_start: 0.5459 (ttp-110) cc_final: 0.5148 (ttp-110) REVERT: p 442 ASP cc_start: 0.6165 (m-30) cc_final: 0.5854 (m-30) REVERT: p 477 SER cc_start: 0.7923 (t) cc_final: 0.7585 (p) REVERT: p 522 LEU cc_start: 0.7867 (mt) cc_final: 0.7312 (mt) REVERT: p 546 GLU cc_start: 0.6229 (mt-10) cc_final: 0.5917 (mt-10) REVERT: p 551 GLU cc_start: 0.7298 (mp0) cc_final: 0.6647 (pm20) REVERT: p 589 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5705 (ttpt) REVERT: p 591 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.5487 (ttm170) REVERT: p 603 MET cc_start: 0.8323 (ptp) cc_final: 0.8032 (mtt) REVERT: p 683 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7273 (mm-40) REVERT: p 728 MET cc_start: 0.6856 (mtm) cc_final: 0.6152 (mtp) REVERT: p 737 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7624 (tp) REVERT: p 796 MET cc_start: 0.8781 (mtm) cc_final: 0.8234 (mtm) REVERT: p 817 GLN cc_start: 0.7579 (tt0) cc_final: 0.6977 (pm20) REVERT: p 827 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6515 (mt-10) REVERT: p 850 ASP cc_start: 0.8241 (t0) cc_final: 0.7962 (t0) REVERT: p 863 ASP cc_start: 0.7468 (m-30) cc_final: 0.6988 (t70) REVERT: p 897 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5090 (mpt-90) REVERT: p 906 GLN cc_start: 0.8270 (tt0) cc_final: 0.7444 (tt0) REVERT: p 959 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7723 (mt-10) REVERT: p 1054 MET cc_start: 0.8027 (mtm) cc_final: 0.7399 (mtt) REVERT: p 1076 GLU cc_start: 0.7207 (tt0) cc_final: 0.6877 (tt0) REVERT: p 1080 ARG cc_start: 0.6556 (mtt90) cc_final: 0.6142 (mtm-85) REVERT: p 1151 MET cc_start: 0.7848 (ptm) cc_final: 0.7459 (ptm) REVERT: p 1165 MET cc_start: 0.6821 (mtm) cc_final: 0.6430 (mtp) REVERT: q 6 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7839 (mm-40) REVERT: q 15 THR cc_start: 0.7561 (m) cc_final: 0.7273 (p) REVERT: q 17 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7047 (pm20) REVERT: q 74 THR cc_start: 0.8369 (m) cc_final: 0.7737 (p) REVERT: q 109 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6923 (pm20) REVERT: q 166 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6451 (mtmt) REVERT: q 199 LYS cc_start: 0.7708 (mttt) cc_final: 0.7484 (mtmt) REVERT: q 202 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7783 (mt-10) REVERT: q 234 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6042 (tt0) REVERT: s 9 ARG cc_start: 0.6008 (mtt180) cc_final: 0.5761 (mtt90) REVERT: s 26 TYR cc_start: 0.7563 (m-80) cc_final: 0.6577 (m-80) REVERT: s 49 SER cc_start: 0.8241 (t) cc_final: 0.7327 (p) REVERT: s 154 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6654 (tt0) REVERT: s 167 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7121 (pt0) REVERT: s 197 SER cc_start: 0.8612 (t) cc_final: 0.8352 (t) REVERT: t 79 VAL cc_start: 0.7058 (t) cc_final: 0.6569 (p) REVERT: t 80 MET cc_start: 0.6981 (mmt) cc_final: 0.6592 (mmt) REVERT: t 81 VAL cc_start: 0.6699 (t) cc_final: 0.6245 (m) REVERT: t 82 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7924 (tm-30) REVERT: t 116 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: u 10 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7821 (mt-10) REVERT: u 16 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.5867 (ptp-170) REVERT: u 24 ASN cc_start: 0.7046 (t0) cc_final: 0.6800 (t0) REVERT: u 119 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: v 4 ILE cc_start: 0.8414 (mt) cc_final: 0.8136 (mm) REVERT: v 37 MET cc_start: 0.7701 (mtp) cc_final: 0.7124 (mtt) REVERT: v 38 ASP cc_start: 0.6062 (OUTLIER) cc_final: 0.5386 (m-30) REVERT: v 63 THR cc_start: 0.8346 (p) cc_final: 0.8046 (t) REVERT: v 100 GLU cc_start: 0.6593 (tt0) cc_final: 0.6035 (mt-10) REVERT: v 102 ASP cc_start: 0.8337 (t0) cc_final: 0.8000 (t0) REVERT: v 136 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7358 (mt-10) REVERT: v 146 LYS cc_start: 0.6492 (tttt) cc_final: 0.6197 (tttp) REVERT: w 28 GLU cc_start: 0.6490 (tt0) cc_final: 0.6045 (pt0) REVERT: w 93 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7570 (mm-30) REVERT: w 122 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6911 (mpp80) REVERT: x 19 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: x 57 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7937 (mm-30) REVERT: x 58 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7270 (mmtt) REVERT: y 8 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7174 (mp0) REVERT: y 23 LYS cc_start: 0.7927 (mttt) cc_final: 0.7423 (mptt) REVERT: y 70 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7642 (ttmm) REVERT: y 103 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7207 (tm-30) REVERT: y 110 LYS cc_start: 0.7397 (tptp) cc_final: 0.7059 (tptp) REVERT: z 16 ILE cc_start: 0.8584 (mt) cc_final: 0.8281 (mm) outliers start: 180 outliers final: 96 residues processed: 633 average time/residue: 1.5480 time to fit residues: 1171.1773 Evaluate side-chains 613 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 491 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 192 ARG Chi-restraints excluded: chain o residue 214 ILE Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 343 LEU Chi-restraints excluded: chain o residue 397 PHE Chi-restraints excluded: chain o residue 423 ASN 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 490 THR Chi-restraints excluded: chain o residue 520 MET Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 632 ASN Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1173 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1341 VAL Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 170 ASP Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 318 LEU Chi-restraints excluded: chain p residue 320 PHE Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 416 ARG Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 541 ILE Chi-restraints excluded: chain p residue 547 GLU Chi-restraints excluded: chain p residue 589 LYS Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 683 GLN Chi-restraints excluded: chain p residue 684 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 737 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 234 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain r residue 38 HIS Chi-restraints excluded: chain s residue 37 LEU Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 116 GLU Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 119 PHE Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 122 ARG Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 302 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 347 optimal weight: 0.0980 chunk 281 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 365 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 143 HIS ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 673 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 935 GLN o1024 ASN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1310 HIS ** o1360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 842 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1094 GLN p1133 HIS ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN ** z 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5502 moved from start: 0.3611 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= 0.187 Angle : 0.444 10.841 49964 Z= 0.236 Chirality : 0.039 0.165 5568 Planarity : 0.003 0.040 6099 Dihedral : 16.710 150.010 5826 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 29.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.41 % Rotamer: Outliers : 4.53 % Allowed : 17.25 % Favored : 78.23 % 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: 2.08 (0.14), residues: 1379 sheet: 0.09 (0.19), residues: 686 loop : -0.11 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP o1192 HIS 0.017 0.001 HIS r 43 PHE 0.015 0.001 PHE p 320 TYR 0.017 0.001 TYR t 115 ARG 0.010 0.000 ARG o1286 *********************** 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 675 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 508 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: o 19 LYS cc_start: 0.7191 (mttp) cc_final: 0.6825 (mmmt) REVERT: o 33 ARG cc_start: 0.7031 (mtm110) cc_final: 0.6698 (mtm-85) REVERT: o 45 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6418 (pm20) REVERT: o 67 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8434 (tpm170) REVERT: o 118 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7348 (mp) REVERT: o 120 ASP cc_start: 0.7164 (m-30) cc_final: 0.6829 (t0) REVERT: o 138 LYS cc_start: 0.7131 (tttm) cc_final: 0.6902 (ttpt) REVERT: o 355 MET cc_start: 0.8522 (mmm) cc_final: 0.8272 (mmm) REVERT: o 447 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7423 (mt-10) REVERT: o 451 CYS cc_start: 0.6288 (m) cc_final: 0.5788 (p) REVERT: o 470 MET cc_start: 0.8560 (mtm) cc_final: 0.8274 (mtp) REVERT: o 473 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5993 (mtm-85) REVERT: o 485 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8126 (t0) REVERT: o 612 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6606 (p0) REVERT: o 660 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7408 (mmm) REVERT: o 673 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6893 (mt0) REVERT: o 700 GLN cc_start: 0.6889 (tt0) cc_final: 0.5972 (tp40) REVERT: o 711 GLN cc_start: 0.6108 (tt0) cc_final: 0.5779 (mm-40) REVERT: o 715 GLU cc_start: 0.6353 (mt-10) cc_final: 0.5970 (mm-30) REVERT: o 796 LYS cc_start: 0.7188 (mttt) cc_final: 0.6849 (mttp) REVERT: o 818 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7376 (mm-30) REVERT: o 868 MET cc_start: 0.7807 (ptt) cc_final: 0.7588 (ptt) REVERT: o 872 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8016 (ttm) REVERT: o 1056 GLU cc_start: 0.6363 (mt-10) cc_final: 0.6089 (pt0) REVERT: o 1085 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6705 (mt-10) REVERT: o 1132 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7860 (mmtm) REVERT: o 1146 GLN cc_start: 0.6634 (pp30) cc_final: 0.6429 (pm20) REVERT: o 1167 ARG cc_start: 0.8023 (ttp-110) cc_final: 0.7497 (ttm-80) REVERT: o 1262 MET cc_start: 0.7644 (ttt) cc_final: 0.6900 (tpp) REVERT: o 1302 GLU cc_start: 0.8278 (pt0) cc_final: 0.7625 (mp0) REVERT: o 1306 LYS cc_start: 0.6502 (mttt) cc_final: 0.5826 (tttp) REVERT: o 1310 HIS cc_start: 0.6796 (p90) cc_final: 0.6329 (p-80) REVERT: o 1325 ASP cc_start: 0.7657 (m-30) cc_final: 0.7288 (p0) REVERT: o 1334 TRP cc_start: 0.8197 (m100) cc_final: 0.7497 (m100) REVERT: o 1339 ASP cc_start: 0.6642 (t0) cc_final: 0.5969 (m-30) REVERT: o 1341 VAL cc_start: 0.8505 (p) cc_final: 0.8012 (t) REVERT: o 1351 ASP cc_start: 0.6685 (m-30) cc_final: 0.6205 (t0) REVERT: o 1364 GLU cc_start: 0.7003 (tp30) cc_final: 0.6332 (tp30) REVERT: o 1383 TYR cc_start: 0.6604 (t80) cc_final: 0.6124 (t80) REVERT: o 1391 SER cc_start: 0.7263 (t) cc_final: 0.6565 (p) REVERT: o 1422 GLN cc_start: 0.7141 (mt0) cc_final: 0.6637 (mm110) REVERT: o 1428 MET cc_start: 0.6116 (ttm) cc_final: 0.5819 (ttm) REVERT: o 1448 SER cc_start: 0.7613 (p) cc_final: 0.7305 (t) REVERT: o 1484 MET cc_start: 0.2738 (ppp) cc_final: 0.2285 (ppp) REVERT: p 21 LEU cc_start: 0.6995 (tp) cc_final: 0.6708 (tt) REVERT: p 23 GLN cc_start: 0.7542 (mm-40) cc_final: 0.7101 (tp40) REVERT: p 109 MET cc_start: 0.7069 (mmm) cc_final: 0.6852 (mmt) REVERT: p 141 GLN cc_start: 0.8555 (pt0) cc_final: 0.7974 (pp30) REVERT: p 143 GLN cc_start: 0.7166 (pt0) cc_final: 0.6916 (pm20) REVERT: p 156 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7860 (mm) REVERT: p 200 MET cc_start: 0.7888 (ttm) cc_final: 0.6610 (tpp) REVERT: p 239 MET cc_start: 0.7068 (ttm) cc_final: 0.6673 (ttm) REVERT: p 254 GLN cc_start: 0.7309 (mt0) cc_final: 0.6913 (pm20) REVERT: p 266 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7564 (mt-10) REVERT: p 291 ASP cc_start: 0.7180 (t0) cc_final: 0.6326 (p0) REVERT: p 299 GLU cc_start: 0.7196 (tp30) cc_final: 0.6507 (tm-30) REVERT: p 309 PHE cc_start: 0.8873 (t80) cc_final: 0.8558 (t80) REVERT: p 318 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7098 (mp) REVERT: p 320 PHE cc_start: 0.8268 (t80) cc_final: 0.7791 (t80) REVERT: p 324 ARG cc_start: 0.8259 (mtt90) cc_final: 0.7763 (mtm-85) REVERT: p 381 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7916 (mt-10) REVERT: p 386 ASP cc_start: 0.6747 (m-30) cc_final: 0.6084 (t0) REVERT: p 394 ASP cc_start: 0.7147 (m-30) cc_final: 0.6879 (m-30) REVERT: p 407 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4680 (mpp) REVERT: p 438 ARG cc_start: 0.5427 (ttp-110) cc_final: 0.5103 (ttp-110) REVERT: p 442 ASP cc_start: 0.6499 (m-30) cc_final: 0.6154 (m-30) REVERT: p 477 SER cc_start: 0.7925 (t) cc_final: 0.7590 (p) REVERT: p 522 LEU cc_start: 0.7820 (mt) cc_final: 0.7290 (mt) REVERT: p 546 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5895 (mt-10) REVERT: p 551 GLU cc_start: 0.7305 (mp0) cc_final: 0.6693 (pm20) REVERT: p 589 LYS cc_start: 0.5979 (OUTLIER) cc_final: 0.5706 (ttpt) REVERT: p 591 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5475 (ttm170) REVERT: p 728 MET cc_start: 0.6782 (mtm) cc_final: 0.6065 (mtp) REVERT: p 745 ASP cc_start: 0.7633 (m-30) cc_final: 0.7321 (m-30) REVERT: p 796 MET cc_start: 0.8821 (mtm) cc_final: 0.8368 (mtm) REVERT: p 827 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6523 (mt-10) REVERT: p 850 ASP cc_start: 0.8235 (t0) cc_final: 0.7953 (t0) REVERT: p 897 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.5110 (mpt-90) REVERT: p 906 GLN cc_start: 0.8175 (tt0) cc_final: 0.7280 (tt0) REVERT: p 959 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7729 (mt-10) REVERT: p 1054 MET cc_start: 0.7977 (mtm) cc_final: 0.7327 (mtt) REVERT: p 1076 GLU cc_start: 0.7190 (tt0) cc_final: 0.6885 (tt0) REVERT: p 1080 ARG cc_start: 0.6548 (mtt90) cc_final: 0.6159 (mtm-85) REVERT: p 1151 MET cc_start: 0.7927 (ptm) cc_final: 0.7563 (ptm) REVERT: p 1165 MET cc_start: 0.6677 (mtm) cc_final: 0.6289 (mtp) REVERT: q 15 THR cc_start: 0.7507 (m) cc_final: 0.7294 (p) REVERT: q 17 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7007 (pm20) REVERT: q 74 THR cc_start: 0.8571 (m) cc_final: 0.7911 (p) REVERT: q 109 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6911 (pm20) REVERT: q 166 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6460 (mtmt) REVERT: q 199 LYS cc_start: 0.7635 (mttt) cc_final: 0.7389 (mtmt) REVERT: q 202 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7769 (mt-10) REVERT: q 234 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5986 (tt0) REVERT: s 26 TYR cc_start: 0.7568 (m-80) cc_final: 0.6580 (m-80) REVERT: s 49 SER cc_start: 0.8224 (t) cc_final: 0.7396 (p) REVERT: s 154 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6675 (tt0) REVERT: s 167 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7185 (pt0) REVERT: s 197 SER cc_start: 0.8705 (t) cc_final: 0.8385 (t) REVERT: t 79 VAL cc_start: 0.6971 (t) cc_final: 0.6347 (p) REVERT: t 80 MET cc_start: 0.6999 (mmt) cc_final: 0.6480 (mmt) REVERT: t 81 VAL cc_start: 0.6753 (t) cc_final: 0.6225 (m) REVERT: t 82 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7996 (tm-30) REVERT: t 116 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: u 10 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7804 (mt-10) REVERT: u 119 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: v 4 ILE cc_start: 0.8418 (mt) cc_final: 0.8136 (mm) REVERT: v 37 MET cc_start: 0.7638 (mtp) cc_final: 0.7085 (mtt) REVERT: v 38 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5436 (m-30) REVERT: v 63 THR cc_start: 0.8303 (p) cc_final: 0.8002 (t) REVERT: v 100 GLU cc_start: 0.6574 (tt0) cc_final: 0.6062 (tt0) REVERT: v 102 ASP cc_start: 0.8349 (t0) cc_final: 0.7986 (t0) REVERT: v 136 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7269 (mt-10) REVERT: w 28 GLU cc_start: 0.6274 (tt0) cc_final: 0.6022 (pt0) REVERT: w 93 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7599 (mm-30) REVERT: w 122 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6957 (mpp80) REVERT: x 19 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: x 47 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7460 (ttp-170) REVERT: x 57 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7952 (mm-30) REVERT: x 58 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7193 (mmtt) REVERT: y 8 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7014 (mp0) REVERT: y 23 LYS cc_start: 0.7947 (mttt) cc_final: 0.7438 (mptt) REVERT: y 70 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7683 (ttmm) REVERT: y 103 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7218 (tm-30) REVERT: y 110 LYS cc_start: 0.7230 (tptp) cc_final: 0.6889 (tptp) REVERT: z 16 ILE cc_start: 0.8675 (mt) cc_final: 0.8391 (mm) outliers start: 167 outliers final: 98 residues processed: 620 average time/residue: 1.5287 time to fit residues: 1136.3518 Evaluate side-chains 611 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 490 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 214 ILE 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 302 VAL Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 343 LEU Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 455 ILE Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 485 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 520 MET Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 660 MET Chi-restraints excluded: chain o residue 673 GLN Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1173 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 156 LEU Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 274 ARG Chi-restraints excluded: chain p residue 318 LEU Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 589 LYS Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 815 LYS Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 234 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 37 LEU Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 116 GLU Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 119 PHE Chi-restraints excluded: chain v residue 23 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 122 ARG Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 47 ARG Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 3.9990 chunk 366 optimal weight: 40.0000 chunk 80 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 407 optimal weight: 1.9990 chunk 338 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN o 143 HIS ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 576 GLN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 935 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1024 ASN o1032 GLN o1146 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS o1263 ASN o1360 ASN o1462 GLN ** p 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 980 HIS p1007 ASN ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS q 260 GLN ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 36632 Z= 0.460 Angle : 0.587 10.413 49964 Z= 0.306 Chirality : 0.044 0.179 5568 Planarity : 0.004 0.050 6099 Dihedral : 16.761 148.921 5824 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 30.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.05 % Favored : 94.75 % Rotamer: Outliers : 5.31 % Allowed : 17.19 % Favored : 77.49 % 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: 0.37 (0.13), residues: 4137 helix: 1.46 (0.14), residues: 1382 sheet: -0.16 (0.19), residues: 694 loop : -0.40 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP q 49 HIS 0.015 0.002 HIS r 43 PHE 0.019 0.002 PHE o 361 TYR 0.020 0.002 TYR o 669 ARG 0.009 0.001 ARG p 592 *********************** 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 698 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 502 time to evaluate : 3.868 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 19 LYS cc_start: 0.6995 (mttp) cc_final: 0.6700 (mmmt) REVERT: o 45 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6545 (pm20) REVERT: o 58 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7879 (ttm) REVERT: o 67 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8415 (tpm170) REVERT: o 118 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7158 (mp) REVERT: o 120 ASP cc_start: 0.7017 (m-30) cc_final: 0.6311 (p0) REVERT: o 138 LYS cc_start: 0.7188 (tttm) cc_final: 0.6952 (ttpt) REVERT: o 355 MET cc_start: 0.8625 (mmm) cc_final: 0.8386 (mmm) REVERT: o 451 CYS cc_start: 0.6524 (m) cc_final: 0.5871 (p) REVERT: o 470 MET cc_start: 0.8438 (mtm) cc_final: 0.8144 (mtp) REVERT: o 473 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6056 (mtm-85) REVERT: o 532 ARG cc_start: 0.6393 (mtm110) cc_final: 0.5828 (ptt180) REVERT: o 659 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: o 687 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8636 (tp) REVERT: o 700 GLN cc_start: 0.7049 (tt0) cc_final: 0.6197 (tp40) REVERT: o 711 GLN cc_start: 0.6091 (tt0) cc_final: 0.5866 (mm-40) REVERT: o 715 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5924 (mm-30) REVERT: o 796 LYS cc_start: 0.7144 (mttt) cc_final: 0.6834 (mttp) REVERT: o 818 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7452 (mm-30) REVERT: o 1056 GLU cc_start: 0.6662 (mt-10) cc_final: 0.6400 (pt0) REVERT: o 1132 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7850 (mmtm) REVERT: o 1144 LEU cc_start: 0.7365 (tp) cc_final: 0.7165 (tp) REVERT: o 1146 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: o 1167 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7535 (ttm-80) REVERT: o 1262 MET cc_start: 0.7544 (ttt) cc_final: 0.7134 (tpp) REVERT: o 1302 GLU cc_start: 0.8133 (pt0) cc_final: 0.7671 (mp0) REVERT: o 1306 LYS cc_start: 0.6536 (mttt) cc_final: 0.5872 (tttp) REVERT: o 1310 HIS cc_start: 0.6760 (p90) cc_final: 0.6185 (p-80) REVERT: o 1322 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.7987 (mm) REVERT: o 1325 ASP cc_start: 0.7610 (m-30) cc_final: 0.7264 (p0) REVERT: o 1329 LYS cc_start: 0.7786 (tttt) cc_final: 0.7521 (ttpp) REVERT: o 1334 TRP cc_start: 0.8193 (m100) cc_final: 0.7336 (m100) REVERT: o 1339 ASP cc_start: 0.6792 (t0) cc_final: 0.5961 (m-30) REVERT: o 1351 ASP cc_start: 0.6466 (m-30) cc_final: 0.6074 (t0) REVERT: o 1364 GLU cc_start: 0.7136 (tp30) cc_final: 0.6364 (tp30) REVERT: o 1383 TYR cc_start: 0.6629 (t80) cc_final: 0.6175 (t80) REVERT: o 1391 SER cc_start: 0.7191 (t) cc_final: 0.6494 (p) REVERT: o 1422 GLN cc_start: 0.7068 (mt0) cc_final: 0.6652 (mm110) REVERT: o 1428 MET cc_start: 0.6746 (ttm) cc_final: 0.6421 (ttm) REVERT: o 1440 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6495 (mmm) REVERT: o 1448 SER cc_start: 0.7622 (p) cc_final: 0.7309 (t) REVERT: o 1484 MET cc_start: 0.2769 (ppp) cc_final: 0.2293 (ppp) REVERT: p 21 LEU cc_start: 0.7032 (tp) cc_final: 0.6768 (tt) REVERT: p 23 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7274 (tp40) REVERT: p 141 GLN cc_start: 0.8598 (pt0) cc_final: 0.7991 (pp30) REVERT: p 143 GLN cc_start: 0.7203 (pt0) cc_final: 0.6886 (pm20) REVERT: p 156 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7953 (mp) REVERT: p 200 MET cc_start: 0.7846 (ttm) cc_final: 0.6504 (tpp) REVERT: p 239 MET cc_start: 0.7155 (ttm) cc_final: 0.6865 (ttm) REVERT: p 254 GLN cc_start: 0.7680 (mt0) cc_final: 0.6773 (pm20) REVERT: p 266 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7560 (mt-10) REVERT: p 291 ASP cc_start: 0.6816 (t0) cc_final: 0.6286 (p0) REVERT: p 299 GLU cc_start: 0.7271 (tp30) cc_final: 0.6541 (tm-30) REVERT: p 309 PHE cc_start: 0.8789 (t80) cc_final: 0.8440 (t80) REVERT: p 320 PHE cc_start: 0.8362 (t80) cc_final: 0.7712 (t80) REVERT: p 324 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7626 (mtm-85) REVERT: p 381 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7890 (mt-10) REVERT: p 386 ASP cc_start: 0.6780 (m-30) cc_final: 0.6076 (t0) REVERT: p 394 ASP cc_start: 0.7312 (m-30) cc_final: 0.6996 (m-30) REVERT: p 407 MET cc_start: 0.5189 (OUTLIER) cc_final: 0.4759 (mpp) REVERT: p 438 ARG cc_start: 0.5505 (ttp-110) cc_final: 0.5161 (ttp-110) REVERT: p 442 ASP cc_start: 0.6180 (m-30) cc_final: 0.5866 (m-30) REVERT: p 477 SER cc_start: 0.8007 (t) cc_final: 0.7684 (p) REVERT: p 522 LEU cc_start: 0.7730 (mt) cc_final: 0.7281 (mt) REVERT: p 551 GLU cc_start: 0.7272 (mp0) cc_final: 0.6846 (pm20) REVERT: p 591 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.5393 (ttm-80) REVERT: p 599 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8159 (t) REVERT: p 684 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6043 (mp0) REVERT: p 728 MET cc_start: 0.6945 (mtm) cc_final: 0.6221 (mtp) REVERT: p 745 ASP cc_start: 0.8164 (m-30) cc_final: 0.7788 (m-30) REVERT: p 796 MET cc_start: 0.8914 (mtm) cc_final: 0.8358 (mtm) REVERT: p 817 GLN cc_start: 0.7513 (tt0) cc_final: 0.6700 (pm20) REVERT: p 827 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6830 (mt-10) REVERT: p 850 ASP cc_start: 0.8270 (t0) cc_final: 0.7986 (t0) REVERT: p 863 ASP cc_start: 0.7517 (m-30) cc_final: 0.7002 (t70) REVERT: p 897 ARG cc_start: 0.6271 (OUTLIER) cc_final: 0.5088 (mpt-90) REVERT: p 906 GLN cc_start: 0.8256 (tt0) cc_final: 0.7339 (tt0) REVERT: p 959 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7646 (mt-10) REVERT: p 1076 GLU cc_start: 0.7257 (tt0) cc_final: 0.6957 (tt0) REVERT: p 1080 ARG cc_start: 0.6384 (mtt90) cc_final: 0.5937 (mtm-85) REVERT: p 1151 MET cc_start: 0.8016 (ptm) cc_final: 0.7629 (ptm) REVERT: p 1165 MET cc_start: 0.6638 (mtm) cc_final: 0.6283 (mtp) REVERT: q 6 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7877 (mm-40) REVERT: q 15 THR cc_start: 0.7411 (m) cc_final: 0.7087 (p) REVERT: q 17 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7015 (pm20) REVERT: q 109 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6707 (pm20) REVERT: q 155 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6949 (tptm) REVERT: q 166 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6643 (mtmt) REVERT: q 234 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6082 (tt0) REVERT: s 8 TYR cc_start: 0.7564 (t80) cc_final: 0.7092 (t80) REVERT: s 13 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6639 (mp) REVERT: s 26 TYR cc_start: 0.7624 (m-80) cc_final: 0.6725 (m-80) REVERT: s 49 SER cc_start: 0.8478 (t) cc_final: 0.7702 (p) REVERT: s 95 GLN cc_start: 0.8567 (tt0) cc_final: 0.8305 (tp-100) REVERT: s 154 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6645 (tt0) REVERT: s 167 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7244 (pt0) REVERT: s 197 SER cc_start: 0.8732 (t) cc_final: 0.8455 (t) REVERT: t 79 VAL cc_start: 0.6966 (t) cc_final: 0.6355 (p) REVERT: t 80 MET cc_start: 0.7074 (mmt) cc_final: 0.6520 (mmt) REVERT: t 81 VAL cc_start: 0.6842 (t) cc_final: 0.6322 (m) REVERT: t 82 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7945 (tm-30) REVERT: u 10 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7765 (mt-10) REVERT: u 16 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6161 (ptp-170) REVERT: u 33 GLU cc_start: 0.7685 (tp30) cc_final: 0.7455 (tm-30) REVERT: u 119 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: v 4 ILE cc_start: 0.8448 (mt) cc_final: 0.8167 (mm) REVERT: v 37 MET cc_start: 0.7686 (mtp) cc_final: 0.7389 (mtt) REVERT: v 38 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5631 (m-30) REVERT: v 63 THR cc_start: 0.8321 (p) cc_final: 0.8042 (t) REVERT: v 100 GLU cc_start: 0.6634 (tt0) cc_final: 0.6119 (tt0) REVERT: v 136 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7325 (mt-10) REVERT: w 21 ASN cc_start: 0.6607 (m-40) cc_final: 0.6309 (m-40) REVERT: w 27 LYS cc_start: 0.3444 (mptt) cc_final: 0.3230 (mptt) REVERT: w 93 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7661 (mm-30) REVERT: x 19 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: x 57 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8032 (mm-30) REVERT: x 58 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7118 (mmtt) REVERT: y 8 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7127 (mp0) REVERT: y 23 LYS cc_start: 0.7943 (mttt) cc_final: 0.7376 (mptt) REVERT: y 70 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7646 (ttmm) REVERT: y 103 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7260 (tm-30) REVERT: y 110 LYS cc_start: 0.7166 (tptp) cc_final: 0.6868 (tptp) REVERT: z 16 ILE cc_start: 0.8683 (mt) cc_final: 0.8414 (mm) outliers start: 196 outliers final: 128 residues processed: 640 average time/residue: 1.5249 time to fit residues: 1171.3030 Evaluate side-chains 634 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 481 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 37 THR Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain o residue 192 ARG Chi-restraints excluded: chain o residue 193 ARG Chi-restraints excluded: chain o residue 214 ILE Chi-restraints excluded: chain o residue 215 LEU 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 290 LEU Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 455 ILE Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 632 ASN Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1173 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1322 ILE Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1341 VAL Chi-restraints excluded: chain o residue 1358 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1440 MET Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 156 LEU Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 223 SER Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 274 ARG Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 416 ARG Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 541 ILE Chi-restraints excluded: chain p residue 547 GLU Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 684 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 910 THR Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1118 VAL Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 234 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain s residue 13 ILE Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 113 SER Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 119 PHE Chi-restraints excluded: chain v residue 23 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 71 ASP Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 101 SER Chi-restraints excluded: chain w residue 122 ARG Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 297 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 342 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 405 optimal weight: 0.0980 chunk 253 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 143 HIS ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 673 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN o 935 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1024 ASN o1146 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS o1445 HIS p 265 GLN ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1094 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN y 89 ASN ** z 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.4015 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= 0.167 Angle : 0.451 13.010 49964 Z= 0.239 Chirality : 0.039 0.163 5568 Planarity : 0.003 0.040 6099 Dihedral : 16.654 148.017 5824 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 4.12 % Allowed : 19.09 % 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: 0.71 (0.13), residues: 4137 helix: 1.91 (0.14), residues: 1378 sheet: -0.03 (0.19), residues: 686 loop : -0.30 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o1192 HIS 0.009 0.001 HIS r 43 PHE 0.016 0.001 PHE o 397 TYR 0.016 0.001 TYR t 115 ARG 0.006 0.000 ARG z 42 *********************** 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 645 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 493 time to evaluate : 3.933 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: S 177 MET cc_start: 0.4975 (tpp) cc_final: 0.4685 (tmm) REVERT: o 19 LYS cc_start: 0.7030 (mttp) cc_final: 0.6692 (mmmt) REVERT: o 45 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6561 (pm20) REVERT: o 67 ARG cc_start: 0.8841 (ttp80) cc_final: 0.8453 (tpm170) REVERT: o 118 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7344 (mp) REVERT: o 120 ASP cc_start: 0.7227 (m-30) cc_final: 0.6475 (p0) REVERT: o 138 LYS cc_start: 0.7132 (tttm) cc_final: 0.6906 (ttpt) REVERT: o 451 CYS cc_start: 0.6397 (m) cc_final: 0.5861 (p) REVERT: o 470 MET cc_start: 0.8494 (mtm) cc_final: 0.8205 (mtp) REVERT: o 473 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5931 (mtm-85) REVERT: o 485 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8166 (t0) REVERT: o 659 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: o 660 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7379 (mmm) REVERT: o 683 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6815 (tm-30) REVERT: o 700 GLN cc_start: 0.6907 (tt0) cc_final: 0.6003 (tp40) REVERT: o 711 GLN cc_start: 0.6084 (tt0) cc_final: 0.5763 (mm-40) REVERT: o 715 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5882 (mm-30) REVERT: o 796 LYS cc_start: 0.7234 (mttt) cc_final: 0.6899 (mttp) REVERT: o 818 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7427 (mm-30) REVERT: o 1056 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6307 (pt0) REVERT: o 1132 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7847 (mmtm) REVERT: o 1144 LEU cc_start: 0.7355 (tp) cc_final: 0.7048 (tm) REVERT: o 1146 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6683 (pp30) REVERT: o 1150 ASP cc_start: 0.7023 (m-30) cc_final: 0.6820 (m-30) REVERT: o 1167 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7529 (ttm-80) REVERT: o 1223 ASP cc_start: 0.8856 (t0) cc_final: 0.8499 (m-30) REVERT: o 1262 MET cc_start: 0.7605 (ttt) cc_final: 0.7126 (tpp) REVERT: o 1279 MET cc_start: 0.6105 (mmp) cc_final: 0.5451 (mtt) REVERT: o 1302 GLU cc_start: 0.8122 (pt0) cc_final: 0.7667 (mp0) REVERT: o 1306 LYS cc_start: 0.6541 (mttt) cc_final: 0.5875 (tttp) REVERT: o 1310 HIS cc_start: 0.6750 (p90) cc_final: 0.6184 (p-80) REVERT: o 1318 LYS cc_start: 0.5769 (mtpt) cc_final: 0.5155 (mtmm) REVERT: o 1325 ASP cc_start: 0.7661 (m-30) cc_final: 0.7344 (p0) REVERT: o 1329 LYS cc_start: 0.7812 (tttt) cc_final: 0.7563 (ttpp) REVERT: o 1334 TRP cc_start: 0.8144 (m100) cc_final: 0.7385 (m100) REVERT: o 1339 ASP cc_start: 0.6825 (t0) cc_final: 0.5989 (m-30) REVERT: o 1351 ASP cc_start: 0.6398 (m-30) cc_final: 0.6099 (t0) REVERT: o 1364 GLU cc_start: 0.7057 (tp30) cc_final: 0.6317 (tp30) REVERT: o 1383 TYR cc_start: 0.6620 (t80) cc_final: 0.6146 (t80) REVERT: o 1391 SER cc_start: 0.7210 (t) cc_final: 0.6509 (p) REVERT: o 1422 GLN cc_start: 0.7100 (mt0) cc_final: 0.6655 (mm110) REVERT: o 1428 MET cc_start: 0.6722 (ttm) cc_final: 0.6345 (ttm) REVERT: o 1448 SER cc_start: 0.7730 (p) cc_final: 0.7368 (t) REVERT: o 1484 MET cc_start: 0.2872 (ppp) cc_final: 0.2397 (ppp) REVERT: p 21 LEU cc_start: 0.6948 (tp) cc_final: 0.6656 (tt) REVERT: p 23 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7125 (tp40) REVERT: p 141 GLN cc_start: 0.8608 (pt0) cc_final: 0.7980 (pp30) REVERT: p 143 GLN cc_start: 0.7180 (pt0) cc_final: 0.6872 (pm20) REVERT: p 200 MET cc_start: 0.7832 (ttm) cc_final: 0.6524 (tpp) REVERT: p 215 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: p 239 MET cc_start: 0.7211 (ttm) cc_final: 0.6836 (ttm) REVERT: p 254 GLN cc_start: 0.7676 (mt0) cc_final: 0.6762 (pm20) REVERT: p 266 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7833 (pp20) REVERT: p 291 ASP cc_start: 0.6993 (t0) cc_final: 0.6386 (p0) REVERT: p 292 PHE cc_start: 0.6913 (m-80) cc_final: 0.6693 (m-80) REVERT: p 299 GLU cc_start: 0.7042 (tp30) cc_final: 0.6432 (tm-30) REVERT: p 309 PHE cc_start: 0.8761 (t80) cc_final: 0.8408 (t80) REVERT: p 320 PHE cc_start: 0.8365 (t80) cc_final: 0.6919 (t80) REVERT: p 324 ARG cc_start: 0.8247 (mtt90) cc_final: 0.6795 (mpt90) REVERT: p 381 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7870 (mt-10) REVERT: p 386 ASP cc_start: 0.6721 (m-30) cc_final: 0.6048 (t0) REVERT: p 394 ASP cc_start: 0.7316 (m-30) cc_final: 0.7001 (m-30) REVERT: p 407 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.4664 (mpp) REVERT: p 438 ARG cc_start: 0.5474 (ttp-110) cc_final: 0.5132 (ttp-110) REVERT: p 442 ASP cc_start: 0.6331 (m-30) cc_final: 0.5998 (m-30) REVERT: p 471 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7511 (t0) REVERT: p 477 SER cc_start: 0.7953 (t) cc_final: 0.7718 (p) REVERT: p 522 LEU cc_start: 0.7782 (mt) cc_final: 0.7325 (mt) REVERT: p 551 GLU cc_start: 0.7195 (mp0) cc_final: 0.6793 (pm20) REVERT: p 572 CYS cc_start: 0.7501 (m) cc_final: 0.6888 (p) REVERT: p 591 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.5552 (ttm170) REVERT: p 599 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8076 (t) REVERT: p 684 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6413 (mp0) REVERT: p 728 MET cc_start: 0.6761 (mtm) cc_final: 0.6062 (mtp) REVERT: p 796 MET cc_start: 0.8964 (mtm) cc_final: 0.8510 (mtm) REVERT: p 827 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6646 (mt-10) REVERT: p 850 ASP cc_start: 0.8263 (t0) cc_final: 0.7981 (t0) REVERT: p 863 ASP cc_start: 0.7498 (m-30) cc_final: 0.6991 (t70) REVERT: p 897 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5130 (mpt-90) REVERT: p 906 GLN cc_start: 0.8254 (tt0) cc_final: 0.7352 (tt0) REVERT: p 959 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7710 (mt-10) REVERT: p 1076 GLU cc_start: 0.7235 (tt0) cc_final: 0.6916 (tt0) REVERT: p 1080 ARG cc_start: 0.6399 (mtt90) cc_final: 0.6020 (mtm-85) REVERT: p 1151 MET cc_start: 0.7948 (ptm) cc_final: 0.7560 (ptm) REVERT: p 1165 MET cc_start: 0.6656 (mtm) cc_final: 0.6320 (mtp) REVERT: q 15 THR cc_start: 0.7389 (m) cc_final: 0.7183 (p) REVERT: q 17 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7023 (pm20) REVERT: q 74 THR cc_start: 0.8513 (m) cc_final: 0.7902 (p) REVERT: q 78 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7028 (tt) REVERT: q 109 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6736 (pm20) REVERT: q 166 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6452 (mtmt) REVERT: r 39 MET cc_start: 0.9307 (ptp) cc_final: 0.9036 (mpm) REVERT: s 26 TYR cc_start: 0.7558 (m-80) cc_final: 0.6611 (m-80) REVERT: s 49 SER cc_start: 0.8490 (t) cc_final: 0.7696 (p) REVERT: s 154 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6665 (tt0) REVERT: s 167 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7402 (pt0) REVERT: s 197 SER cc_start: 0.8668 (t) cc_final: 0.8320 (t) REVERT: t 79 VAL cc_start: 0.6884 (t) cc_final: 0.6280 (p) REVERT: t 80 MET cc_start: 0.7053 (mmt) cc_final: 0.6474 (mmt) REVERT: t 81 VAL cc_start: 0.6837 (t) cc_final: 0.6333 (m) REVERT: t 82 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8038 (tm-30) REVERT: u 10 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7754 (mt-10) REVERT: u 119 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: v 4 ILE cc_start: 0.8420 (mt) cc_final: 0.8136 (mm) REVERT: v 37 MET cc_start: 0.7671 (mtp) cc_final: 0.7269 (mtt) REVERT: v 38 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5505 (m-30) REVERT: v 63 THR cc_start: 0.8293 (p) cc_final: 0.8011 (t) REVERT: v 100 GLU cc_start: 0.6570 (tt0) cc_final: 0.6088 (tt0) REVERT: v 136 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7374 (mt-10) REVERT: v 146 LYS cc_start: 0.6644 (ttmt) cc_final: 0.5745 (ttmm) REVERT: w 93 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7620 (mm-30) REVERT: x 19 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: x 57 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8014 (mm-30) REVERT: x 58 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7126 (mmtt) REVERT: y 8 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7046 (mp0) REVERT: y 23 LYS cc_start: 0.7935 (mttt) cc_final: 0.7322 (mptt) REVERT: y 70 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7675 (ttmm) REVERT: y 103 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7139 (tm-30) REVERT: y 110 LYS cc_start: 0.7201 (tptp) cc_final: 0.6967 (tptp) REVERT: z 16 ILE cc_start: 0.8694 (mt) cc_final: 0.8428 (mm) outliers start: 152 outliers final: 95 residues processed: 597 average time/residue: 1.4905 time to fit residues: 1071.4618 Evaluate side-chains 596 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 480 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 214 ILE Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 485 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 611 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 660 MET Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1085 GLU Chi-restraints excluded: chain o residue 1121 VAL Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1173 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1282 ASP Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1336 LEU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1341 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 108 MET Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 215 TYR Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 274 ARG Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 606 ASP Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 684 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 815 LYS Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 119 PHE Chi-restraints excluded: chain u residue 120 ASP Chi-restraints excluded: chain v residue 23 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 71 ASP Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.0020 chunk 257 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 143 HIS ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN o 935 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1024 ASN o1146 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36632 Z= 0.356 Angle : 0.532 14.688 49964 Z= 0.278 Chirality : 0.042 0.168 5568 Planarity : 0.004 0.054 6099 Dihedral : 16.670 148.268 5824 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 31.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.29 % Favored : 94.51 % Rotamer: Outliers : 4.61 % Allowed : 18.93 % Favored : 76.46 % 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: 0.45 (0.13), residues: 4137 helix: 1.64 (0.14), residues: 1378 sheet: -0.21 (0.19), residues: 690 loop : -0.39 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 49 HIS 0.009 0.001 HIS r 43 PHE 0.019 0.002 PHE p 320 TYR 0.020 0.002 TYR p 388 ARG 0.007 0.000 ARG p 592 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 488 time to evaluate : 3.951 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 19 LYS cc_start: 0.7003 (mttp) cc_final: 0.6751 (tptm) REVERT: o 45 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: o 67 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8413 (tpm170) REVERT: o 118 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7168 (mp) REVERT: o 120 ASP cc_start: 0.7054 (m-30) cc_final: 0.6317 (p0) REVERT: o 138 LYS cc_start: 0.7180 (tttm) cc_final: 0.6952 (ttpt) REVERT: o 451 CYS cc_start: 0.6482 (m) cc_final: 0.5846 (p) REVERT: o 470 MET cc_start: 0.8392 (mtm) cc_final: 0.8087 (mtp) REVERT: o 473 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5906 (mtm-85) REVERT: o 524 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7227 (mmp) REVERT: o 625 ASP cc_start: 0.7954 (t0) cc_final: 0.7661 (t0) REVERT: o 659 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: o 683 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: o 700 GLN cc_start: 0.6972 (tt0) cc_final: 0.6076 (tp40) REVERT: o 711 GLN cc_start: 0.6091 (tt0) cc_final: 0.5784 (mm-40) REVERT: o 715 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5889 (mm-30) REVERT: o 796 LYS cc_start: 0.7174 (mttt) cc_final: 0.6837 (mttp) REVERT: o 818 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7437 (mm-30) REVERT: o 1056 GLU cc_start: 0.6706 (mt-10) cc_final: 0.6405 (pt0) REVERT: o 1132 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7818 (mmtm) REVERT: o 1146 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: o 1167 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7615 (ttm-80) REVERT: o 1223 ASP cc_start: 0.8914 (t0) cc_final: 0.8588 (m-30) REVERT: o 1262 MET cc_start: 0.7597 (ttt) cc_final: 0.7151 (tpp) REVERT: o 1279 MET cc_start: 0.6120 (mmp) cc_final: 0.5377 (mtt) REVERT: o 1302 GLU cc_start: 0.8178 (pt0) cc_final: 0.7895 (mp0) REVERT: o 1306 LYS cc_start: 0.6545 (mttt) cc_final: 0.5876 (tttp) REVERT: o 1318 LYS cc_start: 0.5801 (mtpt) cc_final: 0.5260 (mtmm) REVERT: o 1322 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8056 (mm) REVERT: o 1329 LYS cc_start: 0.7803 (tttt) cc_final: 0.7560 (ttpp) REVERT: o 1334 TRP cc_start: 0.8157 (m100) cc_final: 0.7300 (m100) REVERT: o 1339 ASP cc_start: 0.6790 (t0) cc_final: 0.6003 (m-30) REVERT: o 1351 ASP cc_start: 0.6361 (m-30) cc_final: 0.6140 (t0) REVERT: o 1364 GLU cc_start: 0.7088 (tp30) cc_final: 0.6312 (tp30) REVERT: o 1383 TYR cc_start: 0.6636 (t80) cc_final: 0.6179 (t80) REVERT: o 1391 SER cc_start: 0.7156 (t) cc_final: 0.6418 (p) REVERT: o 1422 GLN cc_start: 0.7055 (mt0) cc_final: 0.6619 (mm110) REVERT: o 1428 MET cc_start: 0.6766 (ttm) cc_final: 0.6403 (ttm) REVERT: o 1448 SER cc_start: 0.7641 (p) cc_final: 0.7348 (t) REVERT: o 1484 MET cc_start: 0.2893 (ppp) cc_final: 0.2402 (ppp) REVERT: p 21 LEU cc_start: 0.7030 (tp) cc_final: 0.6727 (tt) REVERT: p 23 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7220 (tp40) REVERT: p 141 GLN cc_start: 0.8630 (pt0) cc_final: 0.7995 (pp30) REVERT: p 143 GLN cc_start: 0.7236 (pt0) cc_final: 0.6896 (pm20) REVERT: p 156 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7874 (mp) REVERT: p 200 MET cc_start: 0.7837 (ttm) cc_final: 0.6504 (tpp) REVERT: p 215 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5277 (m-80) REVERT: p 254 GLN cc_start: 0.7666 (mt0) cc_final: 0.6758 (pm20) REVERT: p 266 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7815 (pp20) REVERT: p 291 ASP cc_start: 0.6851 (t0) cc_final: 0.6422 (p0) REVERT: p 299 GLU cc_start: 0.7007 (tp30) cc_final: 0.6426 (tm-30) REVERT: p 309 PHE cc_start: 0.8770 (t80) cc_final: 0.8452 (t80) REVERT: p 381 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7887 (mt-10) REVERT: p 386 ASP cc_start: 0.6716 (m-30) cc_final: 0.6106 (t0) REVERT: p 388 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6286 (m-80) REVERT: p 394 ASP cc_start: 0.7396 (m-30) cc_final: 0.7085 (m-30) REVERT: p 407 MET cc_start: 0.5165 (OUTLIER) cc_final: 0.4714 (mpp) REVERT: p 438 ARG cc_start: 0.5567 (ttp-110) cc_final: 0.5231 (ttp-110) REVERT: p 442 ASP cc_start: 0.6185 (m-30) cc_final: 0.5868 (m-30) REVERT: p 471 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7497 (t0) REVERT: p 477 SER cc_start: 0.8003 (t) cc_final: 0.7763 (p) REVERT: p 522 LEU cc_start: 0.7716 (mt) cc_final: 0.7284 (mt) REVERT: p 551 GLU cc_start: 0.7229 (mp0) cc_final: 0.6760 (pm20) REVERT: p 591 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.5426 (ttm170) REVERT: p 599 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8163 (p) REVERT: p 728 MET cc_start: 0.6874 (mtm) cc_final: 0.6159 (mtp) REVERT: p 796 MET cc_start: 0.9015 (mtm) cc_final: 0.8536 (mtm) REVERT: p 817 GLN cc_start: 0.7341 (tt0) cc_final: 0.6605 (pm20) REVERT: p 827 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6752 (mt-10) REVERT: p 850 ASP cc_start: 0.8438 (t0) cc_final: 0.8131 (t0) REVERT: p 863 ASP cc_start: 0.7502 (m-30) cc_final: 0.6994 (t70) REVERT: p 897 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5367 (mpt-90) REVERT: p 906 GLN cc_start: 0.8268 (tt0) cc_final: 0.7317 (tt0) REVERT: p 959 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7646 (mt-10) REVERT: p 1076 GLU cc_start: 0.7224 (tt0) cc_final: 0.6926 (tt0) REVERT: p 1080 ARG cc_start: 0.6319 (mtt90) cc_final: 0.5884 (mtm-85) REVERT: p 1151 MET cc_start: 0.7909 (ptm) cc_final: 0.7531 (ptm) REVERT: p 1165 MET cc_start: 0.6642 (mtm) cc_final: 0.6336 (mtp) REVERT: q 6 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: q 15 THR cc_start: 0.7435 (m) cc_final: 0.7146 (p) REVERT: q 17 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7103 (pm20) REVERT: q 74 THR cc_start: 0.8544 (m) cc_final: 0.7944 (p) REVERT: q 78 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7126 (tt) REVERT: q 109 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6758 (pm20) REVERT: q 166 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6569 (mtmt) REVERT: q 234 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5606 (tt0) REVERT: r 67 TYR cc_start: 0.5141 (OUTLIER) cc_final: 0.4905 (t80) REVERT: s 8 TYR cc_start: 0.7592 (t80) cc_final: 0.7132 (t80) REVERT: s 26 TYR cc_start: 0.7687 (m-80) cc_final: 0.6731 (m-80) REVERT: s 49 SER cc_start: 0.8543 (t) cc_final: 0.7792 (p) REVERT: s 154 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6658 (tt0) REVERT: s 167 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7350 (pt0) REVERT: s 197 SER cc_start: 0.8671 (t) cc_final: 0.8386 (t) REVERT: t 79 VAL cc_start: 0.6991 (t) cc_final: 0.6389 (p) REVERT: t 80 MET cc_start: 0.7086 (mmt) cc_final: 0.6504 (mmt) REVERT: t 81 VAL cc_start: 0.6878 (t) cc_final: 0.6351 (m) REVERT: t 82 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8045 (tm-30) REVERT: u 10 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7810 (mt-10) REVERT: u 119 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: v 4 ILE cc_start: 0.8441 (mt) cc_final: 0.8156 (mm) REVERT: v 28 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6708 (mt) REVERT: v 37 MET cc_start: 0.7647 (mtp) cc_final: 0.7357 (mtt) REVERT: v 38 ASP cc_start: 0.6206 (OUTLIER) cc_final: 0.5608 (m-30) REVERT: v 100 GLU cc_start: 0.6603 (tt0) cc_final: 0.6115 (tt0) REVERT: v 136 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7332 (mt-10) REVERT: w 93 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7666 (mt-10) REVERT: x 19 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: x 57 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8005 (mm-30) REVERT: x 58 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7098 (mmtt) REVERT: y 8 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7070 (mp0) REVERT: y 23 LYS cc_start: 0.7954 (mttt) cc_final: 0.7417 (mptt) REVERT: y 70 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7757 (ttmm) REVERT: y 103 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7258 (tm-30) REVERT: y 110 LYS cc_start: 0.7262 (tptp) cc_final: 0.6864 (tptp) REVERT: z 16 ILE cc_start: 0.8697 (mt) cc_final: 0.8423 (mm) outliers start: 170 outliers final: 123 residues processed: 606 average time/residue: 1.4914 time to fit residues: 1088.3017 Evaluate side-chains 637 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 488 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 192 ARG Chi-restraints excluded: chain o residue 214 ILE 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 302 VAL Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 524 MET Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 611 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 632 ASN Chi-restraints excluded: chain o residue 644 SER Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 792 ASN Chi-restraints excluded: chain o residue 870 SER Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1085 GLU Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1173 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1282 ASP Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1322 ILE Chi-restraints excluded: chain o residue 1336 LEU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1341 VAL Chi-restraints excluded: chain o residue 1352 VAL Chi-restraints excluded: chain o residue 1358 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 156 LEU Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 215 TYR Chi-restraints excluded: chain p residue 223 SER Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 269 ILE Chi-restraints excluded: chain p residue 274 ARG Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1118 VAL Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 234 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain r residue 67 TYR Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 119 PHE Chi-restraints excluded: chain u residue 120 ASP Chi-restraints excluded: chain v residue 23 ASP Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 71 ASP Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 20.0000 chunk 388 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 378 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 296 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 143 HIS ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN o 935 GLN o1024 ASN o1146 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 130 ASN w 21 ASN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN y 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 36632 Z= 0.400 Angle : 0.552 16.607 49964 Z= 0.288 Chirality : 0.042 0.173 5568 Planarity : 0.004 0.056 6099 Dihedral : 16.690 150.345 5824 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 31.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.37 % Favored : 94.42 % Rotamer: Outliers : 4.56 % Allowed : 19.09 % Favored : 76.36 % 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: 1.44 (0.14), residues: 1384 sheet: -0.27 (0.19), residues: 694 loop : -0.50 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP o1192 HIS 0.008 0.001 HIS r 38 PHE 0.017 0.002 PHE o 361 TYR 0.020 0.002 TYR p 388 ARG 0.009 0.001 ARG p 592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 493 time to evaluate : 3.929 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: S 177 MET cc_start: 0.5039 (tpp) cc_final: 0.4755 (tmm) REVERT: o 19 LYS cc_start: 0.7320 (mttp) cc_final: 0.7017 (tptm) REVERT: o 45 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: o 67 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8476 (tpm170) REVERT: o 118 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7078 (mp) REVERT: o 120 ASP cc_start: 0.7071 (m-30) cc_final: 0.6332 (p0) REVERT: o 138 LYS cc_start: 0.7205 (tttm) cc_final: 0.6991 (tttt) REVERT: o 186 ARG cc_start: 0.7929 (mpt-90) cc_final: 0.7379 (mpp80) REVERT: o 451 CYS cc_start: 0.6589 (m) cc_final: 0.5958 (p) REVERT: o 470 MET cc_start: 0.8396 (mtm) cc_final: 0.8099 (mtp) REVERT: o 473 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.6009 (mtm-85) REVERT: o 485 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8211 (t0) REVERT: o 524 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7232 (mmp) REVERT: o 556 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6900 (mm-30) REVERT: o 625 ASP cc_start: 0.7848 (t0) cc_final: 0.7611 (t0) REVERT: o 659 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: o 683 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: o 700 GLN cc_start: 0.6974 (tt0) cc_final: 0.6082 (tp40) REVERT: o 711 GLN cc_start: 0.6123 (tt0) cc_final: 0.5823 (mm-40) REVERT: o 715 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5892 (mm-30) REVERT: o 796 LYS cc_start: 0.7176 (mttt) cc_final: 0.6849 (mttp) REVERT: o 818 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7416 (mm-30) REVERT: o 872 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8046 (ttm) REVERT: o 1024 ASN cc_start: 0.8285 (t0) cc_final: 0.7571 (p0) REVERT: o 1132 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7783 (mmtm) REVERT: o 1146 GLN cc_start: 0.6858 (OUTLIER) cc_final: 0.6383 (pm20) REVERT: o 1167 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7743 (ttm-80) REVERT: o 1223 ASP cc_start: 0.8913 (t0) cc_final: 0.8565 (m-30) REVERT: o 1230 GLN cc_start: 0.7746 (mt0) cc_final: 0.7446 (mp10) REVERT: o 1262 MET cc_start: 0.7584 (ttt) cc_final: 0.7121 (tpp) REVERT: o 1279 MET cc_start: 0.6280 (mmp) cc_final: 0.5560 (mtt) REVERT: o 1302 GLU cc_start: 0.8238 (pt0) cc_final: 0.7726 (pm20) REVERT: o 1306 LYS cc_start: 0.6549 (mttt) cc_final: 0.5875 (tttp) REVERT: o 1318 LYS cc_start: 0.5818 (mtpt) cc_final: 0.5261 (mtmm) REVERT: o 1322 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7770 (mm) REVERT: o 1329 LYS cc_start: 0.7806 (tttt) cc_final: 0.7568 (ttpp) REVERT: o 1334 TRP cc_start: 0.8158 (m100) cc_final: 0.7847 (m100) REVERT: o 1339 ASP cc_start: 0.6794 (t0) cc_final: 0.5994 (m-30) REVERT: o 1351 ASP cc_start: 0.6358 (m-30) cc_final: 0.6157 (t0) REVERT: o 1364 GLU cc_start: 0.7186 (tp30) cc_final: 0.6234 (tp30) REVERT: o 1383 TYR cc_start: 0.6644 (t80) cc_final: 0.6175 (t80) REVERT: o 1422 GLN cc_start: 0.7032 (mt0) cc_final: 0.6632 (mm110) REVERT: o 1428 MET cc_start: 0.6835 (ttm) cc_final: 0.6481 (ttm) REVERT: o 1448 SER cc_start: 0.7637 (p) cc_final: 0.7341 (t) REVERT: o 1484 MET cc_start: 0.2896 (ppp) cc_final: 0.2396 (ppp) REVERT: p 21 LEU cc_start: 0.7031 (tp) cc_final: 0.6762 (tt) REVERT: p 23 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7207 (tp40) REVERT: p 141 GLN cc_start: 0.8635 (pt0) cc_final: 0.8016 (pp30) REVERT: p 143 GLN cc_start: 0.7274 (pt0) cc_final: 0.6909 (pm20) REVERT: p 156 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7878 (mp) REVERT: p 200 MET cc_start: 0.7826 (ttm) cc_final: 0.6529 (tpp) REVERT: p 215 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.5318 (m-80) REVERT: p 254 GLN cc_start: 0.7623 (mt0) cc_final: 0.6742 (pm20) REVERT: p 266 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7799 (pp20) REVERT: p 291 ASP cc_start: 0.6829 (t0) cc_final: 0.6465 (p0) REVERT: p 299 GLU cc_start: 0.7018 (tp30) cc_final: 0.6436 (tm-30) REVERT: p 309 PHE cc_start: 0.8781 (t80) cc_final: 0.8421 (t80) REVERT: p 381 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7891 (mt-10) REVERT: p 386 ASP cc_start: 0.6713 (m-30) cc_final: 0.6102 (t0) REVERT: p 388 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6245 (m-80) REVERT: p 394 ASP cc_start: 0.7457 (m-30) cc_final: 0.7139 (m-30) REVERT: p 407 MET cc_start: 0.5173 (OUTLIER) cc_final: 0.4715 (mpp) REVERT: p 438 ARG cc_start: 0.5581 (ttp-110) cc_final: 0.5174 (tmm160) REVERT: p 442 ASP cc_start: 0.6094 (m-30) cc_final: 0.5720 (m-30) REVERT: p 471 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7495 (t0) REVERT: p 477 SER cc_start: 0.8008 (t) cc_final: 0.7764 (p) REVERT: p 522 LEU cc_start: 0.7712 (mt) cc_final: 0.7280 (mt) REVERT: p 551 GLU cc_start: 0.7217 (mp0) cc_final: 0.6738 (pm20) REVERT: p 591 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.5508 (ttm-80) REVERT: p 599 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8233 (t) REVERT: p 728 MET cc_start: 0.6896 (mtm) cc_final: 0.6177 (mtp) REVERT: p 796 MET cc_start: 0.8978 (mtm) cc_final: 0.8502 (mtm) REVERT: p 817 GLN cc_start: 0.7307 (tt0) cc_final: 0.6688 (pm20) REVERT: p 827 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6869 (mt-10) REVERT: p 850 ASP cc_start: 0.8439 (t0) cc_final: 0.8130 (t0) REVERT: p 863 ASP cc_start: 0.7501 (m-30) cc_final: 0.6996 (t70) REVERT: p 897 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5321 (mpt-90) REVERT: p 959 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7596 (mt-10) REVERT: p 1080 ARG cc_start: 0.6311 (mtt90) cc_final: 0.6003 (mtm-85) REVERT: p 1151 MET cc_start: 0.7922 (ptm) cc_final: 0.7547 (ptm) REVERT: p 1165 MET cc_start: 0.6632 (mtm) cc_final: 0.6311 (mtp) REVERT: q 6 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: q 15 THR cc_start: 0.7436 (m) cc_final: 0.7147 (p) REVERT: q 17 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7105 (pm20) REVERT: q 78 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7169 (tt) REVERT: q 109 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6761 (pm20) REVERT: q 166 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6557 (mtmt) REVERT: q 234 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5653 (tt0) REVERT: s 49 SER cc_start: 0.8681 (t) cc_final: 0.7909 (p) REVERT: s 154 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6656 (tt0) REVERT: s 167 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7375 (pt0) REVERT: s 197 SER cc_start: 0.8676 (t) cc_final: 0.8393 (t) REVERT: t 79 VAL cc_start: 0.6996 (t) cc_final: 0.6382 (p) REVERT: t 80 MET cc_start: 0.7103 (mmt) cc_final: 0.6529 (mmt) REVERT: t 81 VAL cc_start: 0.6930 (t) cc_final: 0.6409 (m) REVERT: t 82 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8022 (tm-30) REVERT: t 116 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7259 (tt0) REVERT: u 10 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7841 (mt-10) REVERT: u 119 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: v 4 ILE cc_start: 0.8533 (mt) cc_final: 0.8268 (mm) REVERT: v 28 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6789 (mt) REVERT: v 37 MET cc_start: 0.7700 (mtp) cc_final: 0.7332 (mtt) REVERT: v 38 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.5786 (m-30) REVERT: v 100 GLU cc_start: 0.6612 (tt0) cc_final: 0.6122 (tt0) REVERT: v 130 ASN cc_start: 0.7922 (t0) cc_final: 0.7476 (t0) REVERT: v 136 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7328 (mt-10) REVERT: w 93 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7813 (mt-10) REVERT: x 19 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: x 58 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7082 (mmtt) REVERT: y 8 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7038 (mp0) REVERT: y 23 LYS cc_start: 0.7894 (mttt) cc_final: 0.7403 (mptt) REVERT: y 70 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7750 (ttmm) REVERT: y 103 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7264 (tm-30) REVERT: y 110 LYS cc_start: 0.7152 (tptp) cc_final: 0.6927 (tptp) REVERT: z 16 ILE cc_start: 0.8701 (mt) cc_final: 0.8430 (mm) outliers start: 168 outliers final: 124 residues processed: 615 average time/residue: 1.4571 time to fit residues: 1080.5339 Evaluate side-chains 634 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 482 time to evaluate : 3.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 192 ARG Chi-restraints excluded: chain o residue 214 ILE 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 302 VAL Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 485 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 524 MET Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 611 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 632 ASN Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 644 SER Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1085 GLU Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1173 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1282 ASP Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1293 LEU Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1322 ILE Chi-restraints excluded: chain o residue 1336 LEU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1341 VAL Chi-restraints excluded: chain o residue 1352 VAL Chi-restraints excluded: chain o residue 1358 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 156 LEU Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 214 LYS Chi-restraints excluded: chain p residue 215 TYR Chi-restraints excluded: chain p residue 223 SER Chi-restraints excluded: chain p residue 232 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 269 ILE Chi-restraints excluded: chain p residue 274 ARG Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 547 GLU Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 763 SER Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 910 THR Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1118 VAL Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 122 SER Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 234 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 119 PHE Chi-restraints excluded: chain v residue 23 ASP Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 63 ASP Chi-restraints excluded: chain w residue 71 ASP Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 101 SER Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.6980 chunk 399 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 chunk 419 optimal weight: 2.9990 chunk 386 optimal weight: 0.7980 chunk 333 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 143 HIS ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 792 ASN o 935 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 650 ASN ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.4306 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= 0.205 Angle : 0.470 18.216 49964 Z= 0.247 Chirality : 0.039 0.164 5568 Planarity : 0.003 0.042 6099 Dihedral : 16.611 152.466 5824 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 32.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 3.80 % Allowed : 20.07 % Favored : 76.14 % 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: 0.52 (0.13), residues: 4137 helix: 1.78 (0.15), residues: 1383 sheet: -0.16 (0.19), residues: 677 loop : -0.42 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o1192 HIS 0.008 0.001 HIS r 43 PHE 0.040 0.001 PHE r 26 TYR 0.020 0.001 TYR u 3 ARG 0.011 0.000 ARG z 42 ********************** 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 629 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 489 time to evaluate : 3.997 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: S 177 MET cc_start: 0.5053 (tpp) cc_final: 0.4781 (tmm) REVERT: o 19 LYS cc_start: 0.7310 (mttp) cc_final: 0.7017 (tptm) REVERT: o 45 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: o 67 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8525 (tpm170) REVERT: o 118 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7186 (mp) REVERT: o 120 ASP cc_start: 0.7089 (m-30) cc_final: 0.6350 (p0) REVERT: o 138 LYS cc_start: 0.7171 (tttm) cc_final: 0.6952 (ttpt) REVERT: o 186 ARG cc_start: 0.7944 (mpt-90) cc_final: 0.7154 (mtm180) REVERT: o 327 ARG cc_start: 0.5768 (mmt-90) cc_final: 0.5542 (mmt-90) REVERT: o 451 CYS cc_start: 0.6382 (m) cc_final: 0.5836 (p) REVERT: o 470 MET cc_start: 0.8483 (mtm) cc_final: 0.8229 (mtp) REVERT: o 473 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5921 (mtm-85) REVERT: o 485 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8151 (t0) REVERT: o 625 ASP cc_start: 0.7893 (t0) cc_final: 0.7659 (t0) REVERT: o 659 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: o 660 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: o 683 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: o 711 GLN cc_start: 0.6119 (tt0) cc_final: 0.5803 (mm-40) REVERT: o 715 GLU cc_start: 0.6239 (mt-10) cc_final: 0.5881 (mm-30) REVERT: o 796 LYS cc_start: 0.7255 (mttt) cc_final: 0.6895 (mttp) REVERT: o 818 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7404 (mm-30) REVERT: o 1024 ASN cc_start: 0.8268 (t0) cc_final: 0.7560 (p0) REVERT: o 1132 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7787 (mmtm) REVERT: o 1146 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6698 (pp30) REVERT: o 1167 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7734 (ttm-80) REVERT: o 1223 ASP cc_start: 0.8918 (t0) cc_final: 0.8568 (m-30) REVERT: o 1262 MET cc_start: 0.7598 (ttt) cc_final: 0.7141 (tpp) REVERT: o 1279 MET cc_start: 0.6327 (mmp) cc_final: 0.5614 (mtt) REVERT: o 1302 GLU cc_start: 0.8254 (pt0) cc_final: 0.7734 (pm20) REVERT: o 1306 LYS cc_start: 0.6550 (mttt) cc_final: 0.5879 (tttp) REVERT: o 1318 LYS cc_start: 0.5713 (mtpt) cc_final: 0.5200 (mtmm) REVERT: o 1329 LYS cc_start: 0.7853 (tttt) cc_final: 0.7607 (ttpp) REVERT: o 1334 TRP cc_start: 0.8136 (m100) cc_final: 0.7370 (m100) REVERT: o 1339 ASP cc_start: 0.6812 (t0) cc_final: 0.6017 (m-30) REVERT: o 1364 GLU cc_start: 0.7114 (tp30) cc_final: 0.6270 (tp30) REVERT: o 1383 TYR cc_start: 0.6633 (t80) cc_final: 0.6164 (t80) REVERT: o 1422 GLN cc_start: 0.7127 (mt0) cc_final: 0.6883 (mm110) REVERT: o 1428 MET cc_start: 0.6768 (ttm) cc_final: 0.6409 (ttm) REVERT: o 1448 SER cc_start: 0.7628 (p) cc_final: 0.7271 (t) REVERT: o 1484 MET cc_start: 0.2694 (ppp) cc_final: 0.2177 (ppp) REVERT: p 21 LEU cc_start: 0.7003 (tp) cc_final: 0.6727 (tt) REVERT: p 23 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7159 (tp40) REVERT: p 141 GLN cc_start: 0.8634 (pt0) cc_final: 0.7973 (pp30) REVERT: p 143 GLN cc_start: 0.7249 (pt0) cc_final: 0.6893 (pm20) REVERT: p 200 MET cc_start: 0.7787 (ttm) cc_final: 0.6531 (tpp) REVERT: p 215 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: p 254 GLN cc_start: 0.7595 (mt0) cc_final: 0.6720 (pm20) REVERT: p 291 ASP cc_start: 0.6706 (t0) cc_final: 0.6353 (p0) REVERT: p 299 GLU cc_start: 0.6955 (tp30) cc_final: 0.6383 (tm-30) REVERT: p 309 PHE cc_start: 0.8765 (t80) cc_final: 0.8403 (t80) REVERT: p 386 ASP cc_start: 0.6685 (m-30) cc_final: 0.6085 (t0) REVERT: p 388 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: p 394 ASP cc_start: 0.7401 (m-30) cc_final: 0.7108 (m-30) REVERT: p 407 MET cc_start: 0.5164 (OUTLIER) cc_final: 0.4661 (mpp) REVERT: p 438 ARG cc_start: 0.5552 (ttp-110) cc_final: 0.5182 (tmm160) REVERT: p 442 ASP cc_start: 0.6091 (m-30) cc_final: 0.5731 (m-30) REVERT: p 471 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7486 (t0) REVERT: p 477 SER cc_start: 0.7972 (t) cc_final: 0.7734 (p) REVERT: p 522 LEU cc_start: 0.7779 (mt) cc_final: 0.7282 (mt) REVERT: p 551 GLU cc_start: 0.7169 (mp0) cc_final: 0.6719 (pm20) REVERT: p 591 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.5582 (ttm170) REVERT: p 599 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8184 (p) REVERT: p 684 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: p 728 MET cc_start: 0.6770 (mtm) cc_final: 0.6092 (mtp) REVERT: p 796 MET cc_start: 0.9023 (mtm) cc_final: 0.8603 (mtm) REVERT: p 827 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6703 (mt-10) REVERT: p 850 ASP cc_start: 0.8312 (t0) cc_final: 0.8045 (t0) REVERT: p 863 ASP cc_start: 0.7484 (m-30) cc_final: 0.6983 (t70) REVERT: p 897 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5460 (mpt-90) REVERT: p 906 GLN cc_start: 0.8265 (tt0) cc_final: 0.7327 (tt0) REVERT: p 959 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7561 (mt-10) REVERT: p 1076 GLU cc_start: 0.7519 (tt0) cc_final: 0.7260 (tt0) REVERT: p 1080 ARG cc_start: 0.6276 (mtt90) cc_final: 0.5861 (mtm-85) REVERT: p 1151 MET cc_start: 0.7961 (ptm) cc_final: 0.7600 (ptm) REVERT: p 1165 MET cc_start: 0.6645 (mtm) cc_final: 0.6330 (mtp) REVERT: q 15 THR cc_start: 0.7396 (m) cc_final: 0.7164 (p) REVERT: q 17 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7007 (pm20) REVERT: q 44 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6388 (pt) REVERT: q 74 THR cc_start: 0.8509 (m) cc_final: 0.7904 (p) REVERT: q 78 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7161 (tt) REVERT: q 109 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6740 (pm20) REVERT: q 166 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6493 (mtmt) REVERT: q 234 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5806 (tt0) REVERT: s 13 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6812 (mp) REVERT: s 154 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6664 (tt0) REVERT: s 167 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7329 (pt0) REVERT: s 197 SER cc_start: 0.8630 (t) cc_final: 0.8286 (t) REVERT: t 79 VAL cc_start: 0.6928 (t) cc_final: 0.6338 (p) REVERT: t 80 MET cc_start: 0.7099 (mmt) cc_final: 0.6510 (mmt) REVERT: t 81 VAL cc_start: 0.6905 (t) cc_final: 0.6386 (m) REVERT: t 82 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8091 (tm-30) REVERT: t 116 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7395 (tt0) REVERT: u 1 MET cc_start: 0.7756 (tpp) cc_final: 0.7070 (tmt) REVERT: u 10 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7823 (mt-10) REVERT: u 119 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: v 4 ILE cc_start: 0.8490 (mt) cc_final: 0.8216 (mm) REVERT: v 37 MET cc_start: 0.7669 (mtp) cc_final: 0.7326 (mtt) REVERT: v 38 ASP cc_start: 0.6191 (OUTLIER) cc_final: 0.5583 (m-30) REVERT: v 100 GLU cc_start: 0.6577 (tt0) cc_final: 0.6110 (tt0) REVERT: v 136 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7304 (mt-10) REVERT: w 93 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7787 (mt-10) REVERT: x 19 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: x 36 ASP cc_start: 0.7657 (m-30) cc_final: 0.7218 (m-30) REVERT: x 58 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7076 (mmtt) REVERT: y 8 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7005 (mp0) REVERT: y 23 LYS cc_start: 0.7930 (mttt) cc_final: 0.7413 (mptt) REVERT: y 70 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7660 (ttmm) REVERT: y 103 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7150 (tm-30) REVERT: y 110 LYS cc_start: 0.7271 (tptp) cc_final: 0.6986 (tptt) REVERT: z 16 ILE cc_start: 0.8710 (mt) cc_final: 0.8437 (mm) outliers start: 140 outliers final: 94 residues processed: 592 average time/residue: 1.5148 time to fit residues: 1079.7277 Evaluate side-chains 599 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 480 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 118 LEU Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 302 VAL Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 473 ARG Chi-restraints excluded: chain o residue 481 THR Chi-restraints excluded: chain o residue 485 ASN Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 611 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 660 MET Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 761 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1173 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1216 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1282 ASP Chi-restraints excluded: chain o residue 1288 ILE Chi-restraints excluded: chain o residue 1295 ASP Chi-restraints excluded: chain o residue 1336 LEU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1341 VAL Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1423 ASP Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 42 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 94 SER Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 167 THR Chi-restraints excluded: chain p residue 187 ILE Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 215 TYR Chi-restraints excluded: chain p residue 223 SER Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 274 ARG Chi-restraints excluded: chain p residue 332 LYS Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 514 THR Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 599 SER Chi-restraints excluded: chain p residue 637 LYS Chi-restraints excluded: chain p residue 640 ILE Chi-restraints excluded: chain p residue 684 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 763 SER Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 794 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 897 ARG Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 958 CYS Chi-restraints excluded: chain p residue 976 MET Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 41 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 53 ASP Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 234 GLU Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain s residue 13 ILE Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain t residue 50 LYS Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 119 PHE Chi-restraints excluded: chain v residue 23 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 52 LEU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 71 ASP Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 101 SER Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 12 LYS Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 58 LYS Chi-restraints excluded: chain y residue 9 SER Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 45 ILE Chi-restraints excluded: chain z residue 30 SER Chi-restraints excluded: chain z residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 307 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 334 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 143 HIS ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 313 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 792 ASN o 935 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 72 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 2 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.173847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119249 restraints weight = 45408.229| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.96 r_work: 0.3177 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4365 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= 0.178 Angle : 0.457 17.871 49964 Z= 0.240 Chirality : 0.039 0.163 5568 Planarity : 0.003 0.041 6099 Dihedral : 16.536 154.083 5824 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 32.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.83 % Favored : 94.97 % Rotamer: Outliers : 3.71 % Allowed : 20.31 % Favored : 75.98 % 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: 0.67 (0.13), residues: 4137 helix: 1.94 (0.15), residues: 1384 sheet: -0.10 (0.19), residues: 687 loop : -0.35 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o1192 HIS 0.008 0.001 HIS r 43 PHE 0.021 0.001 PHE r 26 TYR 0.015 0.001 TYR t 115 ARG 0.010 0.000 ARG z 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17326.91 seconds wall clock time: 305 minutes 37.50 seconds (18337.50 seconds total)