Starting phenix.real_space_refine on Sat Mar 23 05:41:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waz_37410/03_2024/8waz_37410_trim_updated.pdb" } resolution = 2.76 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= 0.005 sd= 0.114 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 22167 2.51 5 N 6281 2.21 5 O 6957 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 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 895": "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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35753 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: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 873 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1118 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 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 4741 SG CYS o 71 114.033 112.551 115.161 1.00141.57 S ATOM 4763 SG CYS o 74 111.808 115.472 115.208 1.00137.29 S ATOM 4810 SG CYS o 81 110.313 111.914 114.951 1.00138.71 S ATOM 5045 SG CYS o 111 101.632 111.244 68.349 1.00164.45 S ATOM 5073 SG CYS o 114 103.712 114.621 68.058 1.00163.67 S ATOM 5419 SG CYS o 184 103.776 111.973 65.262 1.00171.81 S ATOM 24506 SG CYS p1119 105.537 125.011 104.027 1.00141.59 S ATOM 24528 SG CYS p1122 105.435 121.802 101.882 1.00142.57 S ATOM 24643 SG CYS p1137 108.322 122.513 104.009 1.00148.67 S ATOM 24664 SG CYS p1140 107.796 124.351 100.742 1.00152.98 S ATOM 25630 SG CYS q 88 85.436 90.717 173.491 1.00138.12 S ATOM 25643 SG CYS q 90 88.912 89.837 172.318 1.00147.15 S ATOM 25678 SG CYS q 94 87.167 87.472 174.653 1.00132.97 S ATOM 25700 SG CYS q 97 85.736 87.804 171.204 1.00132.45 S ATOM 33006 SG CYS w 17 75.519 52.495 55.827 1.00161.53 S ATOM 33030 SG CYS w 20 78.946 53.532 57.304 1.00163.91 S ATOM 33191 SG CYS w 39 76.758 56.250 56.434 1.00169.29 S ATOM 33216 SG CYS w 42 78.028 54.019 53.634 1.00167.79 S ATOM 33568 SG CYS w 86 44.258 43.124 86.134 1.00150.39 S ATOM 33592 SG CYS w 89 44.868 39.685 87.842 1.00155.57 S ATOM 33796 SG CYS w 114 46.579 42.859 89.127 1.00146.35 S ATOM 33831 SG CYS w 119 47.396 41.279 85.688 1.00152.45 S ATOM 33941 SG CYS x 7 65.564 72.348 151.621 1.00 98.61 S ATOM 33965 SG CYS x 10 63.937 73.321 154.874 1.00 95.35 S ATOM 34229 SG CYS x 44 61.731 72.449 151.697 1.00107.46 S ATOM 34235 SG CYS x 45 63.333 70.079 154.080 1.00108.23 S ATOM 35381 SG CYS z 19 107.138 61.262 142.350 1.00146.64 S ATOM 35400 SG CYS z 22 108.007 58.694 144.870 1.00145.85 S ATOM 35517 SG CYS z 36 110.764 61.210 143.936 1.00153.01 S ATOM 35543 SG CYS z 39 109.456 58.873 141.277 1.00150.68 S Time building chain proxies: 19.08, per 1000 atoms: 0.53 Number of scatterers: 35753 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 6957 8.00 N 6281 7.00 C 22167 6.00 H 23 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.79 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN o2001 " pdb="ZN ZN o2001 " - pdb=" NE2 HIS o 84 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 71 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 74 " pdb="ZN ZN o2001 " - pdb=" SG CYS o 81 " pdb=" ZN o2002 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 184 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 111 " pdb="ZN ZN o2002 " - pdb=" SG CYS o 114 " pdb=" ZN p1202 " pdb="ZN ZN p1202 " - pdb=" SG CYS 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 97 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 88 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 39 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " Number of angles added : 39 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 43 sheets defined 32.7% alpha, 14.9% beta 37 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 15.52 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: 4.167A 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 60 through 62 No H-bonds generated for 'chain 'o' and resid 60 through 62' 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: 4.254A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.879A pdb=" N ARG o 227 " --> pdb=" O GLU o 223 " (cutoff:3.500A) Processing helix chain 'o' and resid 230 through 235 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: 3.631A 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: 4.135A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 540 through 548 Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.810A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.929A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.188A 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 659 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: 4.408A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU o 856 " --> pdb=" O VAL o 852 " (cutoff:3.500A) Processing helix chain 'o' and resid 891 through 893 No H-bonds generated for 'chain 'o' and resid 891 through 893' Processing helix chain 'o' and resid 913 through 920 Processing helix chain 'o' and resid 927 through 933 Processing helix chain 'o' and resid 936 through 944 Processing helix chain 'o' and resid 946 through 969 Processing helix chain 'o' and resid 971 through 973 No H-bonds generated for 'chain 'o' and resid 971 through 973' Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1019 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.128A 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: 3.751A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.074A 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: 3.865A 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: 3.786A 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: 3.866A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) Processing helix chain 'p' and resid 679 through 683 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: 3.733A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 741 removed outlier: 4.641A pdb=" N HIS p 741 " --> pdb=" O THR p 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 738 through 741' Processing helix chain 'p' and resid 762 through 767 Processing helix chain 'p' and resid 798 through 803 Processing helix chain 'p' and resid 969 through 975 Proline residue: p 973 - end of helix Processing helix chain 'p' and resid 978 through 993 Processing helix chain 'p' and resid 1008 through 1018 removed outlier: 3.521A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.859A 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: 4.099A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.586A 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: 4.179A pdb=" N TRP x 18 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU x 19 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.601A 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: 3.563A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.703A 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: 3.843A 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: 6.833A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.009A 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: 3.577A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.154A 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: 11.283A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.678A 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: 3.595A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.399A 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: 4.610A 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: 3.509A 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: 6.096A 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: 3.968A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.113A 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: 3.558A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.186A 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: 3.667A 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: 4.374A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.727A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.248A 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: 6.884A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP p 236 " --> pdb=" O THR p 259 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'p' and resid 484 through 486 Processing sheet with id= W, first strand: chain 'p' and resid 530 through 532 Processing sheet with id= X, first strand: chain 'p' and resid 748 through 751 removed outlier: 3.532A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL p 904 " --> pdb=" O ARG p 924 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'p' and resid 945 through 949 removed outlier: 6.911A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE p1042 " --> pdb=" O ILE p 782 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'p' and resid 827 through 829 Processing sheet with id= AA, first strand: chain 'p' and resid 1113 through 1119 Processing sheet with id= AB, first strand: chain 'p' and resid 1127 through 1129 Processing sheet with id= AC, first strand: chain 'q' and resid 182 through 185 removed outlier: 6.788A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL q 9 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 98 through 106 removed outlier: 6.121A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE q 45 " --> pdb=" O GLY q 168 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 113 through 116 Processing sheet with id= AF, first strand: chain 's' and resid 60 through 62 removed outlier: 6.302A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 's' and resid 147 through 151 removed outlier: 3.709A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL s 190 " --> pdb=" O MET s 151 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 't' and resid 105 through 109 Processing sheet with id= AI, first strand: chain 'u' and resid 2 through 13 removed outlier: 3.559A 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: 5.663A pdb=" N VAL u 45 " --> pdb=" O PHE u 77 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'u' and resid 142 through 146 removed outlier: 7.014A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL u 92 " --> pdb=" O GLY u 96 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLY u 96 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER u 105 " --> pdb=" O ILE u 157 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE u 147 " --> pdb=" O SER u 162 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'u' and resid 127 through 129 Processing sheet with id= AL, first strand: chain 'u' and resid 50 through 54 removed outlier: 6.849A pdb=" N LYS u 71 " --> pdb=" O ASP u 52 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'v' and resid 25 through 31 removed outlier: 5.343A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N HIS v 29 " --> pdb=" O LYS v 13 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'w' and resid 24 through 28 Processing sheet with id= AO, first strand: chain 'w' and resid 79 through 81 Processing sheet with id= AP, first strand: chain 'y' and resid 19 through 23 Processing sheet with id= AQ, first strand: chain 'z' and resid 16 through 18 1147 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 17.33 Time building geometry restraints manager: 15.96 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: 9524 1.33 - 1.49: 11964 1.49 - 1.65: 14822 1.65 - 1.81: 325 Bond restraints: 36658 Sorted by residual: bond pdb=" C2' G2L Z 16 " pdb=" C1' G2L Z 16 " ideal model delta sigma weight residual 1.271 1.522 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C4' G2L Z 16 " pdb=" C3' G2L Z 16 " ideal model delta sigma weight residual 1.270 1.520 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" ND2 ASN N 7 " pdb="HD22 ASN N 7 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N GLY N 5 " pdb=" H GLY N 5 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" N ILE N 4 " pdb=" H ILE N 4 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 ... (remaining 36653 not shown) Histogram of bond angle deviations from ideal: 75.36 - 88.74: 1 88.74 - 102.11: 263 102.11 - 115.49: 24174 115.49 - 128.87: 25289 128.87 - 142.24: 294 Bond angle restraints: 50021 Sorted by residual: angle pdb=" N09 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" O05 W0F p1201 " ideal model delta sigma weight residual 110.18 75.36 34.82 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 110.46 136.33 -25.87 3.00e+00 1.11e-01 7.44e+01 angle pdb=" P26 W0F p1201 " pdb=" O29 W0F p1201 " pdb=" P30 W0F p1201 " ideal model delta sigma weight residual 123.60 142.24 -18.64 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" C10 W0F p1201 " ideal model delta sigma weight residual 99.38 117.53 -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 117.23 109.65 7.58 1.36e+00 5.41e-01 3.11e+01 ... (remaining 50016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.94: 21117 30.94 - 61.88: 988 61.88 - 92.83: 35 92.83 - 123.77: 3 123.77 - 154.71: 1 Dihedral angle restraints: 22144 sinusoidal: 9984 harmonic: 12160 Sorted by residual: dihedral pdb=" O4' C Z 6 " pdb=" C1' C Z 6 " pdb=" N1 C Z 6 " pdb=" C2 C Z 6 " ideal model delta sinusoidal sigma weight residual 200.00 45.29 154.71 1 1.50e+01 4.44e-03 8.12e+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 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU o 343 " pdb=" C LEU o 343 " pdb=" N LYS o 344 " pdb=" CA LYS o 344 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 22141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4922 0.074 - 0.149: 630 0.149 - 0.223: 12 0.223 - 0.298: 1 0.298 - 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 3.05e+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 2.66e+00 ... (remaining 5565 not shown) Planarity restraints: 6103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F p1201 " -0.108 2.00e-02 2.50e+03 4.14e-02 5.15e+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 " 0.007 2.00e-02 2.50e+03 pdb=" C17 W0F p1201 " -0.020 2.00e-02 2.50e+03 pdb=" N09 W0F p1201 " 0.051 2.00e-02 2.50e+03 pdb=" N11 W0F p1201 " 0.012 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 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ILE p 51 " 0.079 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE p 50 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C PHE p 50 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE p 50 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE p 51 " -0.025 2.00e-02 2.50e+03 ... (remaining 6100 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 44 2.37 - 2.93: 15085 2.93 - 3.48: 40954 3.48 - 4.04: 71244 4.04 - 4.60: 102805 Nonbonded interactions: 230132 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.811 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 1.902 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 2.071 2.800 ... (remaining 230127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.780 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: 0.860 Extract box with map and model: 8.740 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 110.790 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5379 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 36635 Z= 0.474 Angle : 0.749 34.821 49969 Z= 0.383 Chirality : 0.047 0.372 5568 Planarity : 0.005 0.076 6099 Dihedral : 15.379 154.710 14271 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.01 % Favored : 95.79 % Rotamer: Outliers : 1.25 % Allowed : 5.94 % Favored : 92.81 % 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: 0.39 (0.13), residues: 4137 helix: 1.17 (0.14), residues: 1421 sheet: 0.21 (0.20), residues: 647 loop : -0.30 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP o1192 HIS 0.006 0.001 HIS q 60 PHE 0.017 0.002 PHE q 63 TYR 0.030 0.002 TYR o 669 ARG 0.008 0.001 ARG t 108 *********************** 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 1022 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 976 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 18 ILE cc_start: 0.7841 (mt) cc_final: 0.7593 (mm) REVERT: o 29 ASP cc_start: 0.7462 (m-30) cc_final: 0.7209 (t0) REVERT: o 31 LEU cc_start: 0.7816 (mt) cc_final: 0.7216 (mt) REVERT: o 37 THR cc_start: 0.7973 (m) cc_final: 0.7391 (t) REVERT: o 54 LEU cc_start: 0.7243 (mt) cc_final: 0.6949 (mm) REVERT: o 58 MET cc_start: 0.7802 (ttp) cc_final: 0.7555 (ttm) REVERT: o 66 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7645 (pt0) REVERT: o 92 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7169 (mtpp) REVERT: o 116 LYS cc_start: 0.7031 (mttt) cc_final: 0.6704 (mttp) REVERT: o 151 LYS cc_start: 0.7410 (mmtp) cc_final: 0.6996 (mmtm) REVERT: o 191 ILE cc_start: 0.7920 (mt) cc_final: 0.7610 (mp) REVERT: o 193 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8178 (tmm-80) REVERT: o 196 LEU cc_start: 0.8514 (mt) cc_final: 0.8173 (mm) REVERT: o 274 ASP cc_start: 0.6134 (t0) cc_final: 0.5882 (t0) REVERT: o 316 THR cc_start: 0.6238 (m) cc_final: 0.6032 (p) REVERT: o 387 ASN cc_start: 0.7495 (m-40) cc_final: 0.7110 (t0) REVERT: o 411 SER cc_start: 0.7659 (m) cc_final: 0.7241 (p) REVERT: o 423 ASN cc_start: 0.8102 (m-40) cc_final: 0.7657 (m110) REVERT: o 495 ASP cc_start: 0.5948 (OUTLIER) cc_final: 0.5346 (p0) REVERT: o 499 ASP cc_start: 0.7382 (m-30) cc_final: 0.7090 (m-30) REVERT: o 520 MET cc_start: 0.7659 (tpt) cc_final: 0.7438 (mmt) REVERT: o 524 MET cc_start: 0.8002 (mmp) cc_final: 0.7605 (mmt) REVERT: o 532 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6124 (ptp90) REVERT: o 552 ASP cc_start: 0.7089 (m-30) cc_final: 0.6799 (m-30) REVERT: o 561 MET cc_start: 0.7844 (mtt) cc_final: 0.7619 (mtt) REVERT: o 583 ARG cc_start: 0.7303 (ptm160) cc_final: 0.7101 (ttp-170) REVERT: o 612 ASP cc_start: 0.6763 (m-30) cc_final: 0.6118 (t0) REVERT: o 634 GLU cc_start: 0.6921 (tt0) cc_final: 0.6353 (mt-10) REVERT: o 700 GLN cc_start: 0.6180 (tt0) cc_final: 0.5831 (tp40) REVERT: o 711 GLN cc_start: 0.5923 (tt0) cc_final: 0.5579 (tp-100) REVERT: o 796 LYS cc_start: 0.6441 (mttt) cc_final: 0.6047 (mtpp) REVERT: o 804 HIS cc_start: 0.7251 (m-70) cc_final: 0.6843 (m170) REVERT: o 818 GLU cc_start: 0.7738 (mt-10) cc_final: 0.6934 (mp0) REVERT: o 841 MET cc_start: 0.6968 (mtp) cc_final: 0.6731 (mtm) REVERT: o 861 GLN cc_start: 0.6573 (tp40) cc_final: 0.6330 (mt0) REVERT: o 868 MET cc_start: 0.7607 (ptt) cc_final: 0.7330 (ptm) REVERT: o 902 GLU cc_start: 0.6368 (tt0) cc_final: 0.6106 (mt-10) REVERT: o 919 LYS cc_start: 0.6710 (mttt) cc_final: 0.6355 (mptp) REVERT: o 926 ASN cc_start: 0.6709 (m-40) cc_final: 0.6152 (t0) REVERT: o 936 GLU cc_start: 0.7298 (tt0) cc_final: 0.6940 (tp30) REVERT: o 997 ASN cc_start: 0.8188 (t0) cc_final: 0.7893 (t0) REVERT: o 1027 ASP cc_start: 0.5867 (m-30) cc_final: 0.5613 (m-30) REVERT: o 1054 MET cc_start: 0.7860 (mmt) cc_final: 0.7496 (mmm) REVERT: o 1136 THR cc_start: 0.8809 (m) cc_final: 0.8517 (p) REVERT: o 1168 LYS cc_start: 0.7546 (mttt) cc_final: 0.6847 (mmtt) REVERT: o 1212 LEU cc_start: 0.6691 (tp) cc_final: 0.6465 (tp) REVERT: o 1233 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8962 (tp30) REVERT: o 1259 ILE cc_start: 0.7166 (mt) cc_final: 0.6799 (mm) REVERT: o 1279 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6155 (mtt) REVERT: o 1306 LYS cc_start: 0.6884 (mttt) cc_final: 0.6024 (mtpp) REVERT: o 1321 ILE cc_start: 0.7818 (mt) cc_final: 0.7436 (pp) REVERT: o 1329 LYS cc_start: 0.7167 (tttt) cc_final: 0.6738 (tttm) REVERT: o 1332 GLN cc_start: 0.7860 (mt0) cc_final: 0.7440 (tt0) REVERT: o 1350 LYS cc_start: 0.6655 (tttm) cc_final: 0.6370 (tttm) REVERT: o 1351 ASP cc_start: 0.7479 (m-30) cc_final: 0.6939 (m-30) REVERT: o 1391 SER cc_start: 0.7117 (t) cc_final: 0.6667 (p) REVERT: o 1412 MET cc_start: 0.7697 (ttp) cc_final: 0.7277 (ttm) REVERT: o 1414 ILE cc_start: 0.8169 (mm) cc_final: 0.7575 (mp) REVERT: o 1417 HIS cc_start: 0.6783 (m-70) cc_final: 0.6548 (m170) REVERT: o 1422 GLN cc_start: 0.7090 (mt0) cc_final: 0.5930 (mm-40) REVERT: o 1423 ASP cc_start: 0.7911 (m-30) cc_final: 0.7392 (t0) REVERT: o 1428 MET cc_start: 0.6976 (ttm) cc_final: 0.6719 (ttm) REVERT: o 1452 LYS cc_start: 0.6991 (mttt) cc_final: 0.6741 (mmtt) REVERT: p 23 GLN cc_start: 0.7179 (mm-40) cc_final: 0.6774 (tp40) REVERT: p 89 GLU cc_start: 0.7330 (tt0) cc_final: 0.6954 (mm-30) REVERT: p 127 ASP cc_start: 0.5751 (m-30) cc_final: 0.5531 (m-30) REVERT: p 151 LYS cc_start: 0.6928 (mttt) cc_final: 0.6587 (mtpp) REVERT: p 200 MET cc_start: 0.7778 (ttm) cc_final: 0.6988 (ttm) REVERT: p 225 LEU cc_start: 0.6779 (tp) cc_final: 0.6382 (tp) REVERT: p 239 MET cc_start: 0.6947 (ttm) cc_final: 0.6659 (ttp) REVERT: p 254 GLN cc_start: 0.5846 (mt0) cc_final: 0.5556 (mp10) REVERT: p 294 ASP cc_start: 0.6626 (t70) cc_final: 0.6030 (t70) REVERT: p 297 MET cc_start: 0.6977 (mtm) cc_final: 0.6502 (mtm) REVERT: p 298 MET cc_start: 0.8104 (mmm) cc_final: 0.7619 (mmt) REVERT: p 304 SER cc_start: 0.7315 (t) cc_final: 0.6972 (m) REVERT: p 309 PHE cc_start: 0.8407 (t80) cc_final: 0.7954 (t80) REVERT: p 345 LYS cc_start: 0.7182 (mptt) cc_final: 0.6921 (mmtm) REVERT: p 361 LYS cc_start: 0.6812 (mttp) cc_final: 0.6605 (mmtm) REVERT: p 386 ASP cc_start: 0.7827 (m-30) cc_final: 0.7454 (m-30) REVERT: p 394 ASP cc_start: 0.6569 (m-30) cc_final: 0.6358 (m-30) REVERT: p 416 ARG cc_start: 0.6409 (mmm-85) cc_final: 0.6190 (mtm-85) REVERT: p 471 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7631 (t0) REVERT: p 574 VAL cc_start: 0.8677 (t) cc_final: 0.8417 (m) REVERT: p 589 LYS cc_start: 0.6438 (mttt) cc_final: 0.5744 (mtpm) REVERT: p 606 ASP cc_start: 0.6708 (t0) cc_final: 0.6430 (t0) REVERT: p 649 ASN cc_start: 0.7707 (t0) cc_final: 0.7169 (t0) REVERT: p 728 MET cc_start: 0.7166 (mtm) cc_final: 0.6849 (mtp) REVERT: p 739 ASN cc_start: 0.7280 (p0) cc_final: 0.6523 (p0) REVERT: p 761 THR cc_start: 0.8364 (m) cc_final: 0.8031 (p) REVERT: p 792 ASP cc_start: 0.7116 (m-30) cc_final: 0.6641 (m-30) REVERT: p 796 MET cc_start: 0.8449 (mtm) cc_final: 0.7950 (mtm) REVERT: p 797 ASN cc_start: 0.7814 (t0) cc_final: 0.7515 (t0) REVERT: p 817 GLN cc_start: 0.6556 (tt0) cc_final: 0.6061 (pm20) REVERT: p 850 ASP cc_start: 0.8306 (t0) cc_final: 0.7957 (p0) REVERT: p 863 ASP cc_start: 0.7495 (m-30) cc_final: 0.7023 (t70) REVERT: p 871 VAL cc_start: 0.7450 (t) cc_final: 0.7111 (p) REVERT: p 892 CYS cc_start: 0.8121 (m) cc_final: 0.7755 (p) REVERT: p 916 TYR cc_start: 0.5438 (m-80) cc_final: 0.5214 (m-80) REVERT: p 952 GLU cc_start: 0.6864 (pt0) cc_final: 0.6544 (pm20) REVERT: p 968 ASN cc_start: 0.8330 (t0) cc_final: 0.8037 (t0) REVERT: p 993 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7686 (tttp) REVERT: p 995 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7090 (pp20) REVERT: p 1054 MET cc_start: 0.7955 (mtm) cc_final: 0.7570 (mtm) REVERT: p 1076 GLU cc_start: 0.7655 (tt0) cc_final: 0.7043 (tt0) REVERT: p 1109 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6052 (mt-10) REVERT: p 1115 GLN cc_start: 0.7950 (mt0) cc_final: 0.7550 (mt0) REVERT: p 1121 LEU cc_start: 0.8219 (mt) cc_final: 0.7962 (mm) REVERT: p 1151 MET cc_start: 0.7963 (ptm) cc_final: 0.7623 (ptm) REVERT: p 1172 MET cc_start: 0.6998 (mmt) cc_final: 0.6778 (mmt) REVERT: q 17 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7363 (mm-30) REVERT: q 93 PHE cc_start: 0.6630 (m-80) cc_final: 0.5603 (m-80) REVERT: q 109 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6013 (pm20) REVERT: q 121 ILE cc_start: 0.7320 (mt) cc_final: 0.7049 (mm) REVERT: q 126 ARG cc_start: 0.7439 (mtt180) cc_final: 0.7097 (mmm-85) REVERT: q 158 GLU cc_start: 0.7079 (tt0) cc_final: 0.6743 (tt0) REVERT: q 225 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7508 (ptmm) REVERT: q 254 LYS cc_start: 0.5699 (tttt) cc_final: 0.5485 (mptt) REVERT: r 32 LEU cc_start: 0.7810 (mt) cc_final: 0.7476 (mm) REVERT: s 49 SER cc_start: 0.8973 (t) cc_final: 0.8644 (p) REVERT: s 70 ASP cc_start: 0.7618 (m-30) cc_final: 0.7289 (t70) REVERT: s 116 GLN cc_start: 0.7821 (mp10) cc_final: 0.7548 (tp-100) REVERT: s 133 GLN cc_start: 0.7124 (mt0) cc_final: 0.6548 (pm20) REVERT: s 138 ASN cc_start: 0.6814 (t0) cc_final: 0.6537 (t0) REVERT: s 158 GLU cc_start: 0.7152 (tt0) cc_final: 0.6585 (pt0) REVERT: s 159 LEU cc_start: 0.7663 (tp) cc_final: 0.7202 (tm) REVERT: s 167 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6412 (pt0) REVERT: s 187 ARG cc_start: 0.7358 (ttt90) cc_final: 0.7099 (ttt-90) REVERT: t 79 VAL cc_start: 0.7568 (t) cc_final: 0.6819 (p) REVERT: t 80 MET cc_start: 0.7342 (mmt) cc_final: 0.5584 (mpt) REVERT: u 44 PHE cc_start: 0.6906 (m-80) cc_final: 0.5809 (m-80) REVERT: u 49 THR cc_start: 0.6969 (m) cc_final: 0.6323 (p) REVERT: v 21 LYS cc_start: 0.7512 (mmtm) cc_final: 0.7109 (mmmm) REVERT: v 26 SER cc_start: 0.8065 (p) cc_final: 0.7679 (m) REVERT: v 37 MET cc_start: 0.7710 (mtp) cc_final: 0.7136 (mtp) REVERT: v 58 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7392 (tp) REVERT: v 63 THR cc_start: 0.8967 (p) cc_final: 0.8689 (t) REVERT: v 76 ASN cc_start: 0.8048 (m-40) cc_final: 0.7678 (m-40) REVERT: v 95 LYS cc_start: 0.7057 (tttt) cc_final: 0.6742 (ttpt) REVERT: v 100 GLU cc_start: 0.6838 (tt0) cc_final: 0.5975 (mt-10) REVERT: v 105 SER cc_start: 0.7636 (t) cc_final: 0.7076 (m) REVERT: v 106 THR cc_start: 0.7234 (p) cc_final: 0.6583 (p) REVERT: v 110 THR cc_start: 0.7501 (p) cc_final: 0.6951 (m) REVERT: v 126 GLN cc_start: 0.7965 (tt0) cc_final: 0.7530 (tt0) REVERT: v 132 LEU cc_start: 0.7603 (mt) cc_final: 0.7390 (mt) REVERT: v 136 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7158 (mt-10) REVERT: v 146 LYS cc_start: 0.6797 (tttt) cc_final: 0.6312 (tptp) REVERT: w 56 ASN cc_start: 0.7412 (t0) cc_final: 0.7192 (t0) REVERT: w 71 ASP cc_start: 0.7711 (m-30) cc_final: 0.7227 (m-30) REVERT: w 93 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7131 (mt-10) REVERT: w 115 THR cc_start: 0.7991 (m) cc_final: 0.7770 (p) REVERT: x 12 LYS cc_start: 0.7110 (ttmt) cc_final: 0.6815 (tttp) REVERT: x 58 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7239 (mtpp) REVERT: y 2 ASN cc_start: 0.8795 (m-40) cc_final: 0.8237 (m110) REVERT: y 7 PHE cc_start: 0.6539 (p90) cc_final: 0.6315 (p90) REVERT: y 8 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6740 (mm-30) REVERT: y 23 LYS cc_start: 0.8174 (mttt) cc_final: 0.7618 (ttmm) REVERT: y 39 ASP cc_start: 0.7026 (p0) cc_final: 0.6688 (p0) REVERT: y 63 VAL cc_start: 0.8309 (t) cc_final: 0.8106 (t) REVERT: y 77 THR cc_start: 0.8683 (p) cc_final: 0.8308 (t) REVERT: y 78 THR cc_start: 0.7892 (p) cc_final: 0.7650 (p) REVERT: z 16 ILE cc_start: 0.7854 (mt) cc_final: 0.7601 (tt) REVERT: z 31 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.7991 (mmp-170) REVERT: z 42 ARG cc_start: 0.7568 (mtt-85) cc_final: 0.6801 (mmt180) REVERT: z 53 VAL cc_start: 0.8178 (t) cc_final: 0.7944 (p) outliers start: 46 outliers final: 10 residues processed: 1005 average time/residue: 1.6779 time to fit residues: 1985.9356 Evaluate side-chains 654 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 640 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 170 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 1279 MET Chi-restraints excluded: chain o residue 1385 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain u residue 147 ILE Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain x residue 16 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 1.9990 chunk 319 optimal weight: 0.0000 chunk 177 optimal weight: 0.0060 chunk 109 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 329 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- 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 72 GLN o 77 ASN o 96 HIS o 181 HIS o 273 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 531 ASN ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 721 HIS o 723 ASN o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN ** o 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 904 GLN o1044 HIS ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1462 GLN p 43 GLN p 111 ASN p 117 ASN p 144 HIS p 164 ASN p 245 GLN p 265 GLN p 315 ASN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 525 ASN p 639 HIS p 683 GLN p 699 HIS ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 838 GLN p 941 GLN p 948 GLN p1021 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 18 ASN ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN r 38 HIS r 66 ASN r 129 GLN s 43 GLN s 210 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 53 ASN u 60 GLN v 44 ASN w 50 ASN w 98 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36635 Z= 0.202 Angle : 0.493 9.952 49969 Z= 0.264 Chirality : 0.040 0.171 5568 Planarity : 0.004 0.052 6099 Dihedral : 16.949 153.078 5841 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Rotamer: Outliers : 3.17 % Allowed : 14.64 % Favored : 82.19 % 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: 0.80 (0.13), residues: 4137 helix: 1.77 (0.14), residues: 1404 sheet: 0.11 (0.19), residues: 694 loop : -0.12 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP o 679 HIS 0.004 0.001 HIS o 465 PHE 0.024 0.001 PHE p 356 TYR 0.014 0.001 TYR s 26 ARG 0.011 0.000 ARG p 380 *********************** 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 765 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 648 time to evaluate : 4.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 18 ILE cc_start: 0.8004 (mt) cc_final: 0.7787 (mm) REVERT: o 31 LEU cc_start: 0.7790 (mt) cc_final: 0.7530 (mt) REVERT: o 37 THR cc_start: 0.8037 (m) cc_final: 0.7582 (t) REVERT: o 58 MET cc_start: 0.7816 (ttp) cc_final: 0.7596 (ttm) REVERT: o 66 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7506 (pt0) REVERT: o 92 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7204 (mtpp) REVERT: o 151 LYS cc_start: 0.7398 (mmtp) cc_final: 0.6909 (mmtm) REVERT: o 193 ARG cc_start: 0.8519 (ttp80) cc_final: 0.7912 (ttp-170) REVERT: o 196 LEU cc_start: 0.8623 (mt) cc_final: 0.8325 (mm) REVERT: o 223 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6457 (mt-10) REVERT: o 226 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6644 (ttpt) REVERT: o 274 ASP cc_start: 0.6266 (t0) cc_final: 0.6038 (t0) REVERT: o 309 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6856 (tp) REVERT: o 316 THR cc_start: 0.6667 (m) cc_final: 0.6387 (p) REVERT: o 387 ASN cc_start: 0.7455 (m-40) cc_final: 0.7028 (t0) REVERT: o 495 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5466 (p0) REVERT: o 520 MET cc_start: 0.7764 (tpt) cc_final: 0.7380 (mmt) REVERT: o 524 MET cc_start: 0.8182 (mmp) cc_final: 0.7316 (mmm) REVERT: o 532 ARG cc_start: 0.6734 (mtm110) cc_final: 0.6077 (ptp90) REVERT: o 552 ASP cc_start: 0.6771 (m-30) cc_final: 0.6471 (m-30) REVERT: o 612 ASP cc_start: 0.6846 (m-30) cc_final: 0.6046 (t0) REVERT: o 634 GLU cc_start: 0.6953 (tt0) cc_final: 0.6298 (mt-10) REVERT: o 683 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6313 (tt0) REVERT: o 700 GLN cc_start: 0.6625 (tt0) cc_final: 0.6112 (tp40) REVERT: o 711 GLN cc_start: 0.5994 (tt0) cc_final: 0.5615 (tp-100) REVERT: o 728 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.7144 (t) REVERT: o 743 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5526 (ttm110) REVERT: o 796 LYS cc_start: 0.6513 (mttt) cc_final: 0.6156 (mtpp) REVERT: o 804 HIS cc_start: 0.7362 (m-70) cc_final: 0.7045 (m170) REVERT: o 818 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7022 (mp0) REVERT: o 841 MET cc_start: 0.6757 (mtp) cc_final: 0.6504 (mtm) REVERT: o 857 THR cc_start: 0.6208 (p) cc_final: 0.5962 (p) REVERT: o 861 GLN cc_start: 0.6643 (tp40) cc_final: 0.6259 (mt0) REVERT: o 902 GLU cc_start: 0.6394 (tt0) cc_final: 0.6115 (mt-10) REVERT: o 919 LYS cc_start: 0.6675 (mttt) cc_final: 0.6378 (mptp) REVERT: o 1054 MET cc_start: 0.7760 (mmt) cc_final: 0.7420 (mmm) REVERT: o 1085 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6344 (mm-30) REVERT: o 1136 THR cc_start: 0.8929 (m) cc_final: 0.8685 (t) REVERT: o 1168 LYS cc_start: 0.7614 (mttt) cc_final: 0.7167 (mptt) REVERT: o 1233 GLU cc_start: 0.9223 (mm-30) cc_final: 0.9002 (tp30) REVERT: o 1244 ASN cc_start: 0.6083 (t0) cc_final: 0.5309 (m-40) REVERT: o 1259 ILE cc_start: 0.7104 (mt) cc_final: 0.6732 (mm) REVERT: o 1279 MET cc_start: 0.6667 (mtm) cc_final: 0.6417 (mtt) REVERT: o 1306 LYS cc_start: 0.6849 (mttt) cc_final: 0.5952 (mmmt) REVERT: o 1321 ILE cc_start: 0.7767 (mt) cc_final: 0.7364 (pp) REVERT: o 1329 LYS cc_start: 0.7003 (tttt) cc_final: 0.6662 (tttm) REVERT: o 1332 GLN cc_start: 0.7787 (mt0) cc_final: 0.7361 (tt0) REVERT: o 1351 ASP cc_start: 0.7651 (m-30) cc_final: 0.7376 (m-30) REVERT: o 1364 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5813 (mm-30) REVERT: o 1391 SER cc_start: 0.7518 (t) cc_final: 0.7034 (p) REVERT: o 1412 MET cc_start: 0.7702 (ttp) cc_final: 0.7173 (ttm) REVERT: o 1414 ILE cc_start: 0.7744 (mm) cc_final: 0.7396 (mp) REVERT: o 1417 HIS cc_start: 0.7221 (m-70) cc_final: 0.6999 (m170) REVERT: o 1422 GLN cc_start: 0.7059 (mt0) cc_final: 0.5850 (mm110) REVERT: o 1423 ASP cc_start: 0.7952 (m-30) cc_final: 0.7323 (t0) REVERT: o 1452 LYS cc_start: 0.7242 (mttt) cc_final: 0.6894 (mmtm) REVERT: o 1479 LYS cc_start: 0.6266 (OUTLIER) cc_final: 0.5528 (mppt) REVERT: o 1484 MET cc_start: 0.3552 (ppp) cc_final: 0.3331 (ppp) REVERT: p 23 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6788 (tp40) REVERT: p 117 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7856 (m-40) REVERT: p 200 MET cc_start: 0.7774 (ttm) cc_final: 0.7098 (ttm) REVERT: p 239 MET cc_start: 0.6707 (ttm) cc_final: 0.6422 (ttp) REVERT: p 254 GLN cc_start: 0.6009 (mt0) cc_final: 0.5580 (mp10) REVERT: p 304 SER cc_start: 0.7083 (t) cc_final: 0.6750 (m) REVERT: p 309 PHE cc_start: 0.8458 (t80) cc_final: 0.8064 (t80) REVERT: p 345 LYS cc_start: 0.7396 (mptt) cc_final: 0.7139 (mmtm) REVERT: p 361 LYS cc_start: 0.6370 (mttp) cc_final: 0.6060 (mmtm) REVERT: p 386 ASP cc_start: 0.7793 (m-30) cc_final: 0.7421 (m-30) REVERT: p 416 ARG cc_start: 0.6451 (mmm-85) cc_final: 0.6250 (ttp-110) REVERT: p 420 GLN cc_start: 0.6157 (tp40) cc_final: 0.5909 (tp-100) REVERT: p 471 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7569 (t0) REVERT: p 497 LYS cc_start: 0.7676 (tptp) cc_final: 0.7432 (tptt) REVERT: p 508 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.5388 (mtt) REVERT: p 574 VAL cc_start: 0.8696 (t) cc_final: 0.8400 (m) REVERT: p 589 LYS cc_start: 0.5575 (mttt) cc_final: 0.5102 (ttmt) REVERT: p 593 GLN cc_start: 0.5874 (OUTLIER) cc_final: 0.5084 (mp10) REVERT: p 606 ASP cc_start: 0.6580 (t0) cc_final: 0.5927 (t0) REVERT: p 609 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5250 (mt-10) REVERT: p 728 MET cc_start: 0.7451 (mtm) cc_final: 0.7095 (mtp) REVERT: p 761 THR cc_start: 0.8349 (m) cc_final: 0.7951 (p) REVERT: p 764 MET cc_start: 0.7898 (mtt) cc_final: 0.7323 (mtp) REVERT: p 770 ARG cc_start: 0.7316 (mtm110) cc_final: 0.6859 (mtm-85) REVERT: p 796 MET cc_start: 0.8522 (mtm) cc_final: 0.8070 (mtm) REVERT: p 797 ASN cc_start: 0.7774 (t0) cc_final: 0.7460 (t0) REVERT: p 817 GLN cc_start: 0.6733 (tt0) cc_final: 0.6358 (pm20) REVERT: p 863 ASP cc_start: 0.7316 (m-30) cc_final: 0.6979 (t70) REVERT: p 952 GLU cc_start: 0.6845 (pt0) cc_final: 0.6640 (pm20) REVERT: p 993 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7650 (tttp) REVERT: p 995 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7219 (OUTLIER) REVERT: p 1054 MET cc_start: 0.8254 (mtm) cc_final: 0.7888 (mtm) REVERT: p 1076 GLU cc_start: 0.7227 (tt0) cc_final: 0.6999 (tt0) REVERT: p 1081 ASP cc_start: 0.7365 (t0) cc_final: 0.7075 (t0) REVERT: p 1090 GLU cc_start: 0.6698 (mp0) cc_final: 0.6469 (mp0) REVERT: p 1109 GLU cc_start: 0.6365 (mm-30) cc_final: 0.6022 (mt-10) REVERT: p 1121 LEU cc_start: 0.8223 (mt) cc_final: 0.7998 (mm) REVERT: p 1151 MET cc_start: 0.7892 (ptm) cc_final: 0.7645 (ptm) REVERT: p 1172 MET cc_start: 0.7009 (mmt) cc_final: 0.6520 (mmt) REVERT: q 17 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7204 (mm-30) REVERT: q 61 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: q 109 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6179 (pm20) REVERT: q 121 ILE cc_start: 0.7195 (mt) cc_final: 0.6938 (mp) REVERT: q 126 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7151 (mmm-85) REVERT: q 158 GLU cc_start: 0.7036 (tt0) cc_final: 0.6547 (tt0) REVERT: q 225 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7655 (ptmm) REVERT: q 234 GLU cc_start: 0.7684 (tt0) cc_final: 0.7434 (tt0) REVERT: s 49 SER cc_start: 0.9069 (t) cc_final: 0.8680 (p) REVERT: s 70 ASP cc_start: 0.7605 (m-30) cc_final: 0.7401 (t70) REVERT: s 133 GLN cc_start: 0.6963 (mt0) cc_final: 0.6395 (pm20) REVERT: s 158 GLU cc_start: 0.7210 (tt0) cc_final: 0.6615 (pt0) REVERT: s 159 LEU cc_start: 0.7653 (tp) cc_final: 0.7199 (tm) REVERT: s 167 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6422 (pt0) REVERT: t 80 MET cc_start: 0.6551 (mmt) cc_final: 0.6042 (mpt) REVERT: t 116 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7398 (mt-10) REVERT: u 16 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.5685 (ptp-170) REVERT: v 11 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6552 (m-30) REVERT: v 26 SER cc_start: 0.8084 (p) cc_final: 0.7745 (m) REVERT: v 37 MET cc_start: 0.7771 (mtp) cc_final: 0.7183 (mtp) REVERT: v 55 LYS cc_start: 0.7161 (mttp) cc_final: 0.6533 (ttmm) REVERT: v 58 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7153 (tt) REVERT: v 63 THR cc_start: 0.8919 (p) cc_final: 0.8642 (t) REVERT: v 74 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7101 (tm-30) REVERT: v 76 ASN cc_start: 0.7768 (m-40) cc_final: 0.7467 (m-40) REVERT: v 95 LYS cc_start: 0.7153 (tttt) cc_final: 0.6685 (ttpt) REVERT: v 100 GLU cc_start: 0.6637 (tt0) cc_final: 0.5779 (mt-10) REVERT: v 105 SER cc_start: 0.7385 (t) cc_final: 0.7171 (m) REVERT: v 106 THR cc_start: 0.7046 (p) cc_final: 0.6675 (p) REVERT: v 132 LEU cc_start: 0.7537 (mt) cc_final: 0.7309 (mt) REVERT: v 136 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6866 (mt-10) REVERT: v 142 TYR cc_start: 0.8223 (m-80) cc_final: 0.7931 (m-80) REVERT: v 146 LYS cc_start: 0.6781 (tttt) cc_final: 0.6263 (tptp) REVERT: w 23 MET cc_start: 0.8157 (ttp) cc_final: 0.7531 (ttp) REVERT: w 71 ASP cc_start: 0.7587 (m-30) cc_final: 0.7245 (m-30) REVERT: w 93 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7088 (mt-10) REVERT: w 109 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7422 (ptm160) REVERT: w 115 THR cc_start: 0.8058 (m) cc_final: 0.7700 (p) REVERT: x 58 LYS cc_start: 0.7625 (mmtt) cc_final: 0.7274 (mtpp) REVERT: y 8 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6768 (mm-30) REVERT: y 23 LYS cc_start: 0.8198 (mttt) cc_final: 0.7699 (ttmp) REVERT: y 77 THR cc_start: 0.8827 (p) cc_final: 0.8390 (t) REVERT: y 78 THR cc_start: 0.8140 (p) cc_final: 0.7843 (p) REVERT: y 111 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7097 (t0) REVERT: y 114 GLU cc_start: 0.7294 (pp20) cc_final: 0.7060 (pp20) REVERT: z 28 ILE cc_start: 0.8976 (mt) cc_final: 0.8684 (mp) REVERT: z 42 ARG cc_start: 0.7218 (mtt-85) cc_final: 0.6850 (mmt180) REVERT: z 44 MET cc_start: 0.7503 (mmp) cc_final: 0.7184 (mmt) outliers start: 117 outliers final: 51 residues processed: 718 average time/residue: 1.5881 time to fit residues: 1358.2318 Evaluate side-chains 641 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 574 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 347 GLU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 743 ARG Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1139 LEU Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1472 ASP Chi-restraints excluded: chain o residue 1479 LYS Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 117 ASN Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 344 GLN Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 421 LYS Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 593 GLN Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 644 LYS Chi-restraints excluded: chain p residue 666 ASP Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1164 SER Chi-restraints excluded: chain q residue 27 ASP Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 147 ILE Chi-restraints excluded: chain v residue 11 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 58 LEU Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 111 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 318 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 383 optimal weight: 0.6980 chunk 413 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 379 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 ASN o 273 GLN o 301 HIS ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 576 GLN o 723 ASN o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 904 GLN o1044 HIS o1163 HIS o1220 HIS o1310 HIS ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 98 HIS ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 649 ASN p 683 GLN p 718 GLN ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 980 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN s 116 GLN s 210 GLN t 46 GLN ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 126 GLN w 22 ASN w 45 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36635 Z= 0.225 Angle : 0.481 11.543 49969 Z= 0.257 Chirality : 0.040 0.208 5568 Planarity : 0.003 0.050 6099 Dihedral : 16.763 150.722 5829 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.01 % Rotamer: Outliers : 3.90 % Allowed : 15.97 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4137 helix: 1.87 (0.14), residues: 1416 sheet: 0.10 (0.19), residues: 701 loop : -0.14 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 479 HIS 0.004 0.001 HIS x 52 PHE 0.017 0.001 PHE u 2 TYR 0.024 0.001 TYR u 3 ARG 0.007 0.000 ARG p 255 *********************** 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 722 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 578 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 18 ILE cc_start: 0.8088 (mt) cc_final: 0.7882 (mm) REVERT: o 31 LEU cc_start: 0.7624 (mt) cc_final: 0.7392 (mt) REVERT: o 37 THR cc_start: 0.8196 (m) cc_final: 0.7787 (t) REVERT: o 58 MET cc_start: 0.7822 (ttp) cc_final: 0.7605 (ttm) REVERT: o 66 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7504 (pt0) REVERT: o 92 LYS cc_start: 0.7560 (mtpp) cc_final: 0.7345 (mmmm) REVERT: o 116 LYS cc_start: 0.7450 (mttt) cc_final: 0.7017 (mttp) REVERT: o 119 VAL cc_start: 0.8089 (t) cc_final: 0.7615 (m) REVERT: o 139 LYS cc_start: 0.6872 (ttmt) cc_final: 0.6460 (mmtt) REVERT: o 151 LYS cc_start: 0.7327 (mmtp) cc_final: 0.6798 (mmtm) REVERT: o 193 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8132 (tmm-80) REVERT: o 226 LYS cc_start: 0.7078 (mtpt) cc_final: 0.6619 (mtpp) REVERT: o 229 SER cc_start: 0.6060 (t) cc_final: 0.5661 (p) REVERT: o 309 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6882 (tp) REVERT: o 316 THR cc_start: 0.6802 (m) cc_final: 0.6566 (p) REVERT: o 387 ASN cc_start: 0.7444 (m-40) cc_final: 0.7074 (t0) REVERT: o 495 ASP cc_start: 0.6257 (p0) cc_final: 0.5969 (p0) REVERT: o 524 MET cc_start: 0.8191 (mmp) cc_final: 0.7178 (mmm) REVERT: o 532 ARG cc_start: 0.6707 (mtm110) cc_final: 0.6111 (ptp90) REVERT: o 634 GLU cc_start: 0.6923 (tt0) cc_final: 0.6274 (mt-10) REVERT: o 683 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6216 (tt0) REVERT: o 700 GLN cc_start: 0.6617 (tt0) cc_final: 0.6144 (tp40) REVERT: o 711 GLN cc_start: 0.5784 (tt0) cc_final: 0.5413 (tp-100) REVERT: o 728 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7078 (t) REVERT: o 738 GLU cc_start: 0.5673 (mm-30) cc_final: 0.5434 (tp30) REVERT: o 743 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5842 (ttm110) REVERT: o 796 LYS cc_start: 0.6748 (mttt) cc_final: 0.6368 (mtpp) REVERT: o 818 GLU cc_start: 0.7822 (mt-10) cc_final: 0.6925 (pm20) REVERT: o 857 THR cc_start: 0.6112 (p) cc_final: 0.5869 (p) REVERT: o 861 GLN cc_start: 0.6571 (tp40) cc_final: 0.6252 (mt0) REVERT: o 919 LYS cc_start: 0.6591 (mttt) cc_final: 0.6339 (mptp) REVERT: o 1054 MET cc_start: 0.7717 (mmt) cc_final: 0.7460 (mmm) REVERT: o 1085 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6227 (mm-30) REVERT: o 1136 THR cc_start: 0.8981 (m) cc_final: 0.8739 (p) REVERT: o 1168 LYS cc_start: 0.7691 (mttt) cc_final: 0.6976 (mmtt) REVERT: o 1219 LYS cc_start: 0.7886 (tppp) cc_final: 0.7625 (tppp) REVERT: o 1244 ASN cc_start: 0.6729 (t0) cc_final: 0.6083 (m-40) REVERT: o 1259 ILE cc_start: 0.7162 (mt) cc_final: 0.6818 (mm) REVERT: o 1279 MET cc_start: 0.6646 (mtm) cc_final: 0.6387 (mtt) REVERT: o 1306 LYS cc_start: 0.6899 (mttt) cc_final: 0.5947 (mmmt) REVERT: o 1321 ILE cc_start: 0.7434 (mt) cc_final: 0.7195 (pp) REVERT: o 1329 LYS cc_start: 0.7051 (tttt) cc_final: 0.6651 (tttp) REVERT: o 1332 GLN cc_start: 0.8017 (mt0) cc_final: 0.7524 (tt0) REVERT: o 1351 ASP cc_start: 0.7660 (m-30) cc_final: 0.7385 (m-30) REVERT: o 1364 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5780 (mm-30) REVERT: o 1372 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7199 (mm-30) REVERT: o 1412 MET cc_start: 0.7806 (ttp) cc_final: 0.7304 (tmm) REVERT: o 1417 HIS cc_start: 0.7233 (m-70) cc_final: 0.6928 (m-70) REVERT: o 1422 GLN cc_start: 0.6850 (mt0) cc_final: 0.5913 (mm110) REVERT: o 1452 LYS cc_start: 0.7128 (mttt) cc_final: 0.6820 (mmtm) REVERT: o 1479 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5289 (mppt) REVERT: p 23 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6903 (tp40) REVERT: p 144 HIS cc_start: 0.7302 (m90) cc_final: 0.6927 (m-70) REVERT: p 200 MET cc_start: 0.7933 (ttm) cc_final: 0.7193 (ttm) REVERT: p 239 MET cc_start: 0.6639 (ttm) cc_final: 0.6340 (ttp) REVERT: p 254 GLN cc_start: 0.5969 (mt0) cc_final: 0.5596 (mp10) REVERT: p 304 SER cc_start: 0.6989 (t) cc_final: 0.6625 (m) REVERT: p 309 PHE cc_start: 0.8452 (t80) cc_final: 0.8112 (t80) REVERT: p 312 GLN cc_start: 0.6962 (tm-30) cc_final: 0.6719 (tm-30) REVERT: p 344 GLN cc_start: 0.7608 (tt0) cc_final: 0.7259 (tt0) REVERT: p 345 LYS cc_start: 0.7434 (mptt) cc_final: 0.7123 (mmtm) REVERT: p 386 ASP cc_start: 0.8126 (m-30) cc_final: 0.7656 (m-30) REVERT: p 497 LYS cc_start: 0.7751 (tptp) cc_final: 0.7226 (tptt) REVERT: p 508 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.5645 (mtt) REVERT: p 574 VAL cc_start: 0.8662 (t) cc_final: 0.8381 (m) REVERT: p 589 LYS cc_start: 0.5809 (mttt) cc_final: 0.5259 (mtpm) REVERT: p 593 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5093 (mp10) REVERT: p 606 ASP cc_start: 0.6699 (t0) cc_final: 0.5929 (t0) REVERT: p 609 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5436 (mt-10) REVERT: p 616 THR cc_start: 0.5821 (OUTLIER) cc_final: 0.5567 (t) REVERT: p 647 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: p 728 MET cc_start: 0.7443 (mtm) cc_final: 0.6983 (mtp) REVERT: p 761 THR cc_start: 0.8433 (m) cc_final: 0.8049 (p) REVERT: p 764 MET cc_start: 0.7917 (mtt) cc_final: 0.7347 (mtp) REVERT: p 770 ARG cc_start: 0.7286 (mtm110) cc_final: 0.6968 (mtm-85) REVERT: p 796 MET cc_start: 0.8506 (mtm) cc_final: 0.8149 (mtm) REVERT: p 863 ASP cc_start: 0.7398 (m-30) cc_final: 0.7004 (t70) REVERT: p 931 ILE cc_start: 0.7729 (pt) cc_final: 0.7408 (pp) REVERT: p 995 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7000 (pt0) REVERT: p 1022 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7006 (tp) REVERT: p 1054 MET cc_start: 0.8269 (mtm) cc_final: 0.7868 (mtm) REVERT: p 1076 GLU cc_start: 0.7219 (tt0) cc_final: 0.6946 (tt0) REVERT: p 1081 ASP cc_start: 0.7368 (t0) cc_final: 0.7126 (t0) REVERT: p 1090 GLU cc_start: 0.6616 (mp0) cc_final: 0.6415 (mp0) REVERT: p 1109 GLU cc_start: 0.6455 (mm-30) cc_final: 0.6216 (mt-10) REVERT: p 1114 TYR cc_start: 0.7915 (t80) cc_final: 0.7435 (t80) REVERT: p 1121 LEU cc_start: 0.8237 (mt) cc_final: 0.8013 (mm) REVERT: p 1138 ARG cc_start: 0.7175 (mtt-85) cc_final: 0.6832 (mtp85) REVERT: p 1151 MET cc_start: 0.7985 (ptm) cc_final: 0.7712 (ptm) REVERT: p 1172 MET cc_start: 0.7008 (mmt) cc_final: 0.6530 (mmt) REVERT: q 17 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7427 (tt0) REVERT: q 109 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6269 (pm20) REVERT: q 121 ILE cc_start: 0.7142 (mt) cc_final: 0.6865 (mp) REVERT: q 126 ARG cc_start: 0.7651 (mtt180) cc_final: 0.7202 (mmm-85) REVERT: q 158 GLU cc_start: 0.6980 (tt0) cc_final: 0.6413 (tt0) REVERT: q 225 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7508 (pttm) REVERT: s 43 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: s 49 SER cc_start: 0.8897 (t) cc_final: 0.8392 (p) REVERT: s 116 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7517 (tp-100) REVERT: s 133 GLN cc_start: 0.7328 (mt0) cc_final: 0.6527 (pm20) REVERT: s 158 GLU cc_start: 0.7304 (tt0) cc_final: 0.6691 (pt0) REVERT: s 167 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6989 (mt-10) REVERT: t 80 MET cc_start: 0.6516 (mmt) cc_final: 0.6040 (mpt) REVERT: t 116 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7397 (mt-10) REVERT: u 1 MET cc_start: 0.7944 (tmm) cc_final: 0.7617 (tmm) REVERT: u 16 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.5739 (ptp-170) REVERT: v 4 ILE cc_start: 0.8266 (mt) cc_final: 0.8066 (mm) REVERT: v 11 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: v 37 MET cc_start: 0.7752 (mtp) cc_final: 0.7153 (mtp) REVERT: v 55 LYS cc_start: 0.7142 (mttp) cc_final: 0.6573 (ttmm) REVERT: v 63 THR cc_start: 0.8901 (p) cc_final: 0.8639 (t) REVERT: v 74 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7339 (tm-30) REVERT: v 76 ASN cc_start: 0.7814 (m-40) cc_final: 0.7540 (m-40) REVERT: v 95 LYS cc_start: 0.7317 (tttt) cc_final: 0.6868 (ttpt) REVERT: v 100 GLU cc_start: 0.6381 (tt0) cc_final: 0.5567 (mt-10) REVERT: v 132 LEU cc_start: 0.7353 (mt) cc_final: 0.7099 (mt) REVERT: v 146 LYS cc_start: 0.6718 (tttt) cc_final: 0.6180 (tptp) REVERT: w 18 GLN cc_start: 0.8150 (mt0) cc_final: 0.7917 (pp30) REVERT: w 93 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7138 (mt-10) REVERT: w 109 ARG cc_start: 0.7854 (ttm-80) cc_final: 0.7630 (ptm160) REVERT: w 115 THR cc_start: 0.7826 (m) cc_final: 0.7440 (p) REVERT: x 58 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7225 (mtpp) REVERT: y 8 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6842 (mm-30) REVERT: y 23 LYS cc_start: 0.8219 (mttt) cc_final: 0.7600 (ttmm) REVERT: y 77 THR cc_start: 0.9045 (p) cc_final: 0.8533 (t) REVERT: y 85 GLU cc_start: 0.6408 (tt0) cc_final: 0.6126 (tt0) REVERT: y 111 ASP cc_start: 0.7645 (m-30) cc_final: 0.7200 (t0) REVERT: z 42 ARG cc_start: 0.7165 (mtt-85) cc_final: 0.6891 (mmm160) REVERT: z 44 MET cc_start: 0.7784 (mmp) cc_final: 0.7451 (mmt) outliers start: 144 outliers final: 73 residues processed: 667 average time/residue: 1.6309 time to fit residues: 1297.4840 Evaluate side-chains 642 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 553 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 347 GLU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 683 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 743 ARG Chi-restraints excluded: chain o residue 782 SER Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1479 LYS Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 100 GLU Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 579 ASP Chi-restraints excluded: chain p residue 593 GLN Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1130 THR Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain s residue 43 GLN Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 116 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 VAL Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 49 THR Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 147 ILE Chi-restraints excluded: chain u residue 157 ILE Chi-restraints excluded: chain v residue 11 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU 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 96 SER Chi-restraints excluded: chain z residue 53 VAL 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: 3.9990 chunk 198 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 384 optimal weight: 2.9990 chunk 406 optimal weight: 0.0870 chunk 200 optimal weight: 0.0970 chunk 364 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 539 GLN o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 265 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 43 GLN s 210 GLN t 46 GLN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 130 ASN w 22 ASN w 50 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36635 Z= 0.227 Angle : 0.470 9.884 49969 Z= 0.250 Chirality : 0.040 0.164 5568 Planarity : 0.003 0.049 6099 Dihedral : 16.655 149.619 5823 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.16 % Favored : 95.67 % Rotamer: Outliers : 3.93 % Allowed : 16.46 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.13), residues: 4137 helix: 1.89 (0.14), residues: 1422 sheet: 0.12 (0.19), residues: 689 loop : -0.18 (0.14), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 143 HIS 0.004 0.001 HIS p 387 PHE 0.021 0.001 PHE s 40 TYR 0.014 0.001 TYR o 413 ARG 0.005 0.000 ARG p 255 *********************** 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 708 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 563 time to evaluate : 4.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 111 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6417 (mppt) REVERT: o 18 ILE cc_start: 0.8131 (mt) cc_final: 0.7913 (mm) REVERT: o 31 LEU cc_start: 0.7369 (mt) cc_final: 0.7107 (mt) REVERT: o 37 THR cc_start: 0.8303 (m) cc_final: 0.7640 (p) REVERT: o 58 MET cc_start: 0.7814 (ttp) cc_final: 0.7597 (ttm) REVERT: o 66 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7500 (pt0) REVERT: o 92 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7469 (mmmm) REVERT: o 119 VAL cc_start: 0.8103 (t) cc_final: 0.7619 (m) REVERT: o 139 LYS cc_start: 0.6839 (ttmt) cc_final: 0.6390 (mmtt) REVERT: o 151 LYS cc_start: 0.7336 (mmtp) cc_final: 0.6646 (mmtm) REVERT: o 193 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8202 (tmm-80) REVERT: o 226 LYS cc_start: 0.7073 (mtpt) cc_final: 0.6618 (mtpp) REVERT: o 229 SER cc_start: 0.6387 (t) cc_final: 0.6049 (p) REVERT: o 309 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6905 (tp) REVERT: o 316 THR cc_start: 0.6999 (m) cc_final: 0.6670 (p) REVERT: o 317 MET cc_start: 0.7170 (ttp) cc_final: 0.6960 (ttt) REVERT: o 495 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6115 (p0) REVERT: o 524 MET cc_start: 0.8172 (mmp) cc_final: 0.7182 (mmm) REVERT: o 532 ARG cc_start: 0.6681 (mtm110) cc_final: 0.6096 (ptp90) REVERT: o 634 GLU cc_start: 0.6925 (tt0) cc_final: 0.6240 (mt-10) REVERT: o 683 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6168 (tt0) REVERT: o 700 GLN cc_start: 0.6518 (tt0) cc_final: 0.5950 (tp40) REVERT: o 711 GLN cc_start: 0.5769 (tt0) cc_final: 0.5410 (tp-100) REVERT: o 728 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7150 (t) REVERT: o 738 GLU cc_start: 0.5511 (mm-30) cc_final: 0.5270 (tp30) REVERT: o 743 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5829 (ttm110) REVERT: o 796 LYS cc_start: 0.6853 (mttt) cc_final: 0.6490 (mtpp) REVERT: o 818 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6708 (pm20) REVERT: o 861 GLN cc_start: 0.6594 (tp40) cc_final: 0.6226 (mt0) REVERT: o 919 LYS cc_start: 0.6597 (mttt) cc_final: 0.6281 (mptp) REVERT: o 1054 MET cc_start: 0.7714 (mmt) cc_final: 0.7443 (mmm) REVERT: o 1085 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6027 (mm-30) REVERT: o 1136 THR cc_start: 0.8997 (m) cc_final: 0.8749 (p) REVERT: o 1168 LYS cc_start: 0.7407 (mttt) cc_final: 0.6746 (mmtm) REVERT: o 1219 LYS cc_start: 0.7901 (tppp) cc_final: 0.7614 (tppp) REVERT: o 1244 ASN cc_start: 0.6725 (t0) cc_final: 0.6100 (m-40) REVERT: o 1259 ILE cc_start: 0.7135 (mt) cc_final: 0.6798 (mm) REVERT: o 1279 MET cc_start: 0.6653 (mtm) cc_final: 0.6385 (mtt) REVERT: o 1306 LYS cc_start: 0.6935 (mttt) cc_final: 0.5912 (mmmt) REVERT: o 1321 ILE cc_start: 0.7404 (mt) cc_final: 0.7143 (pp) REVERT: o 1329 LYS cc_start: 0.7105 (tttt) cc_final: 0.6710 (tttp) REVERT: o 1332 GLN cc_start: 0.8263 (mt0) cc_final: 0.7815 (tt0) REVERT: o 1351 ASP cc_start: 0.7743 (m-30) cc_final: 0.7383 (m-30) REVERT: o 1364 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5799 (mm-30) REVERT: o 1372 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7233 (mm-30) REVERT: o 1412 MET cc_start: 0.7800 (ttp) cc_final: 0.7320 (tmm) REVERT: o 1417 HIS cc_start: 0.7304 (m-70) cc_final: 0.7092 (m170) REVERT: o 1422 GLN cc_start: 0.6800 (mt0) cc_final: 0.5889 (mm110) REVERT: o 1479 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5242 (mppt) REVERT: p 23 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7080 (tp40) REVERT: p 92 TYR cc_start: 0.6832 (m-80) cc_final: 0.6494 (m-80) REVERT: p 200 MET cc_start: 0.7980 (ttm) cc_final: 0.7188 (ttm) REVERT: p 239 MET cc_start: 0.6580 (ttm) cc_final: 0.6329 (ttp) REVERT: p 254 GLN cc_start: 0.5953 (mt0) cc_final: 0.5543 (mp10) REVERT: p 304 SER cc_start: 0.7053 (t) cc_final: 0.6720 (m) REVERT: p 309 PHE cc_start: 0.8556 (t80) cc_final: 0.8217 (t80) REVERT: p 344 GLN cc_start: 0.7488 (tt0) cc_final: 0.7281 (tt0) REVERT: p 386 ASP cc_start: 0.8127 (m-30) cc_final: 0.7634 (m-30) REVERT: p 407 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5716 (mtp) REVERT: p 471 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7504 (t0) REVERT: p 497 LYS cc_start: 0.7726 (tptp) cc_final: 0.7464 (tptp) REVERT: p 508 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.5608 (mtt) REVERT: p 561 ILE cc_start: 0.5658 (OUTLIER) cc_final: 0.5431 (mt) REVERT: p 574 VAL cc_start: 0.8682 (t) cc_final: 0.8415 (m) REVERT: p 589 LYS cc_start: 0.5792 (mttt) cc_final: 0.5262 (mtpm) REVERT: p 593 GLN cc_start: 0.6087 (OUTLIER) cc_final: 0.5204 (mp10) REVERT: p 606 ASP cc_start: 0.6722 (t0) cc_final: 0.5991 (t0) REVERT: p 609 GLU cc_start: 0.6004 (mm-30) cc_final: 0.5479 (mt-10) REVERT: p 616 THR cc_start: 0.5952 (OUTLIER) cc_final: 0.5693 (t) REVERT: p 647 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6103 (pm20) REVERT: p 728 MET cc_start: 0.7441 (mtm) cc_final: 0.6967 (mtp) REVERT: p 761 THR cc_start: 0.8458 (m) cc_final: 0.8073 (p) REVERT: p 764 MET cc_start: 0.7972 (mtt) cc_final: 0.7391 (mtp) REVERT: p 796 MET cc_start: 0.8521 (mtm) cc_final: 0.8185 (mtm) REVERT: p 863 ASP cc_start: 0.7480 (m-30) cc_final: 0.7112 (t70) REVERT: p 931 ILE cc_start: 0.7681 (pt) cc_final: 0.7349 (pp) REVERT: p 995 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7001 (pt0) REVERT: p 1022 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7001 (tp) REVERT: p 1054 MET cc_start: 0.8259 (mtm) cc_final: 0.7834 (mtm) REVERT: p 1072 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6323 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7339 (tt0) cc_final: 0.7120 (tt0) REVERT: p 1081 ASP cc_start: 0.7115 (t0) cc_final: 0.6860 (t0) REVERT: p 1109 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6291 (mt-10) REVERT: p 1114 TYR cc_start: 0.7887 (t80) cc_final: 0.7505 (t80) REVERT: p 1121 LEU cc_start: 0.8186 (mt) cc_final: 0.7962 (mm) REVERT: p 1131 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7788 (ptp-170) REVERT: p 1151 MET cc_start: 0.8013 (ptm) cc_final: 0.7730 (ptm) REVERT: p 1172 MET cc_start: 0.7069 (mmt) cc_final: 0.6672 (mmt) REVERT: q 17 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7473 (tt0) REVERT: q 103 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7867 (tp) REVERT: q 109 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6347 (pm20) REVERT: q 126 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7260 (mmm-85) REVERT: q 158 GLU cc_start: 0.6796 (tt0) cc_final: 0.6258 (pt0) REVERT: q 166 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6407 (mtmt) REVERT: q 225 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7590 (pttm) REVERT: s 49 SER cc_start: 0.8866 (t) cc_final: 0.8349 (p) REVERT: s 106 VAL cc_start: 0.6984 (t) cc_final: 0.6666 (m) REVERT: s 133 GLN cc_start: 0.7408 (mt0) cc_final: 0.7128 (mm-40) REVERT: s 158 GLU cc_start: 0.7200 (tt0) cc_final: 0.6643 (pt0) REVERT: s 167 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7029 (mt-10) REVERT: u 1 MET cc_start: 0.7935 (tmm) cc_final: 0.7486 (tmm) REVERT: u 16 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6115 (ptp-170) REVERT: u 101 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6439 (mp) REVERT: u 104 MET cc_start: 0.6873 (tpp) cc_final: 0.5923 (tpp) REVERT: u 147 ILE cc_start: 0.9327 (mp) cc_final: 0.9113 (tp) REVERT: v 11 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6498 (m-30) REVERT: v 37 MET cc_start: 0.7788 (mtp) cc_final: 0.7215 (mtp) REVERT: v 55 LYS cc_start: 0.7141 (mttp) cc_final: 0.6516 (ttmm) REVERT: v 63 THR cc_start: 0.8898 (p) cc_final: 0.8642 (t) REVERT: v 74 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7360 (tp30) REVERT: v 76 ASN cc_start: 0.7852 (m-40) cc_final: 0.7545 (m-40) REVERT: v 95 LYS cc_start: 0.7284 (tttt) cc_final: 0.6872 (ttpt) REVERT: v 100 GLU cc_start: 0.6537 (tt0) cc_final: 0.5691 (mt-10) REVERT: v 103 GLU cc_start: 0.7683 (pm20) cc_final: 0.7403 (pm20) REVERT: v 132 LEU cc_start: 0.7259 (mt) cc_final: 0.7020 (mt) REVERT: v 146 LYS cc_start: 0.6746 (tttt) cc_final: 0.6222 (tptp) REVERT: v 147 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7711 (mmmm) REVERT: w 93 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7155 (tt0) REVERT: w 109 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7661 (ptm160) REVERT: w 115 THR cc_start: 0.7546 (m) cc_final: 0.7056 (p) REVERT: x 19 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: x 58 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7241 (mtpp) REVERT: y 8 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6865 (mm-30) REVERT: y 23 LYS cc_start: 0.8199 (mttt) cc_final: 0.7674 (ttmm) REVERT: y 55 GLN cc_start: 0.7513 (mt0) cc_final: 0.6819 (mt0) REVERT: y 77 THR cc_start: 0.9058 (p) cc_final: 0.8521 (t) REVERT: y 85 GLU cc_start: 0.6424 (tt0) cc_final: 0.6144 (tt0) REVERT: y 111 ASP cc_start: 0.7627 (m-30) cc_final: 0.7242 (t0) REVERT: z 42 ARG cc_start: 0.7260 (mtt-85) cc_final: 0.6979 (mmm160) outliers start: 145 outliers final: 84 residues processed: 649 average time/residue: 1.5603 time to fit residues: 1207.1077 Evaluate side-chains 641 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 534 time to evaluate : 5.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 347 GLU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 743 ARG Chi-restraints excluded: chain o residue 782 SER Chi-restraints excluded: chain o residue 847 LEU Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1479 LYS Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 593 GLN Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 896 LEU Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 1004 ASP Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1130 THR Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 VAL Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 11 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 110 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 55 LEU Chi-restraints excluded: chain y residue 14 GLU 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 96 SER Chi-restraints excluded: chain y residue 97 GLU Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 5 optimal weight: 40.0000 chunk 302 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 347 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 365 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 27 ASN ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN o 757 GLN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN o1220 HIS ** o1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN p 430 ASN p 649 ASN p 654 GLN p 749 HIS ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 262 GLN s 64 HIS s 98 ASN s 116 GLN s 210 GLN t 46 GLN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 53 ASN v 130 ASN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36635 Z= 0.276 Angle : 0.502 10.813 49969 Z= 0.265 Chirality : 0.041 0.168 5568 Planarity : 0.004 0.053 6099 Dihedral : 16.568 148.104 5819 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 27.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 4.39 % Allowed : 16.78 % Favored : 78.82 % 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: 0.74 (0.13), residues: 4137 helix: 1.78 (0.14), residues: 1426 sheet: 0.03 (0.19), residues: 688 loop : -0.22 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 679 HIS 0.009 0.001 HIS r 43 PHE 0.015 0.001 PHE q 63 TYR 0.016 0.002 TYR p 811 ARG 0.006 0.000 ARG p 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 558 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 111 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6393 (mppt) REVERT: o 37 THR cc_start: 0.8367 (m) cc_final: 0.7697 (p) REVERT: o 66 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7422 (pt0) REVERT: o 92 LYS cc_start: 0.7796 (mtpp) cc_final: 0.7246 (mtpp) REVERT: o 119 VAL cc_start: 0.8023 (t) cc_final: 0.7542 (m) REVERT: o 139 LYS cc_start: 0.6891 (ttmt) cc_final: 0.6453 (mmtt) REVERT: o 151 LYS cc_start: 0.7332 (mmtp) cc_final: 0.6839 (mmtm) REVERT: o 193 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8335 (tmm-80) REVERT: o 229 SER cc_start: 0.6360 (t) cc_final: 0.6133 (p) REVERT: o 240 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.8044 (Cg_exo) REVERT: o 309 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6951 (tp) REVERT: o 316 THR cc_start: 0.6981 (m) cc_final: 0.6649 (p) REVERT: o 317 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7060 (ttt) REVERT: o 445 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6304 (mtmm) REVERT: o 520 MET cc_start: 0.7751 (mmt) cc_final: 0.7242 (mmt) REVERT: o 524 MET cc_start: 0.8216 (mmp) cc_final: 0.7153 (mmm) REVERT: o 532 ARG cc_start: 0.6665 (mtm110) cc_final: 0.6080 (ptp90) REVERT: o 634 GLU cc_start: 0.7055 (tt0) cc_final: 0.6238 (mt-10) REVERT: o 683 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: o 700 GLN cc_start: 0.6546 (tt0) cc_final: 0.5982 (tp40) REVERT: o 711 GLN cc_start: 0.5777 (tt0) cc_final: 0.5449 (tp-100) REVERT: o 728 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.6905 (t) REVERT: o 743 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5874 (ttm110) REVERT: o 796 LYS cc_start: 0.6986 (mttt) cc_final: 0.6573 (mtpp) REVERT: o 861 GLN cc_start: 0.6600 (tp40) cc_final: 0.6211 (mt0) REVERT: o 919 LYS cc_start: 0.6644 (mttt) cc_final: 0.6271 (mptp) REVERT: o 1054 MET cc_start: 0.7728 (mmt) cc_final: 0.7442 (mmm) REVERT: o 1136 THR cc_start: 0.9017 (m) cc_final: 0.8772 (p) REVERT: o 1168 LYS cc_start: 0.7445 (mttt) cc_final: 0.6927 (mptt) REVERT: o 1219 LYS cc_start: 0.7957 (tppp) cc_final: 0.7654 (tppp) REVERT: o 1233 GLU cc_start: 0.9224 (tp30) cc_final: 0.8954 (tp30) REVERT: o 1259 ILE cc_start: 0.7066 (mt) cc_final: 0.6719 (mm) REVERT: o 1279 MET cc_start: 0.6681 (mtm) cc_final: 0.6429 (mtt) REVERT: o 1306 LYS cc_start: 0.6809 (mttt) cc_final: 0.5877 (mmmt) REVERT: o 1321 ILE cc_start: 0.7189 (mt) cc_final: 0.6857 (pp) REVERT: o 1329 LYS cc_start: 0.7442 (tttt) cc_final: 0.6997 (tttm) REVERT: o 1332 GLN cc_start: 0.8327 (mt0) cc_final: 0.7962 (tt0) REVERT: o 1351 ASP cc_start: 0.7741 (m-30) cc_final: 0.7473 (m-30) REVERT: o 1364 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5838 (mm-30) REVERT: o 1372 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7234 (mm-30) REVERT: o 1412 MET cc_start: 0.7830 (ttp) cc_final: 0.7385 (tmm) REVERT: o 1422 GLN cc_start: 0.6727 (mt0) cc_final: 0.5890 (mm110) REVERT: p 144 HIS cc_start: 0.7314 (m90) cc_final: 0.7036 (m-70) REVERT: p 200 MET cc_start: 0.7915 (ttm) cc_final: 0.7111 (ttm) REVERT: p 239 MET cc_start: 0.6436 (ttm) cc_final: 0.6195 (ttp) REVERT: p 254 GLN cc_start: 0.5777 (mt0) cc_final: 0.5281 (mp10) REVERT: p 304 SER cc_start: 0.7112 (t) cc_final: 0.6781 (m) REVERT: p 309 PHE cc_start: 0.8542 (t80) cc_final: 0.8218 (t80) REVERT: p 344 GLN cc_start: 0.7468 (tt0) cc_final: 0.7254 (tt0) REVERT: p 386 ASP cc_start: 0.7915 (m-30) cc_final: 0.7346 (m-30) REVERT: p 471 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7469 (t0) REVERT: p 508 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.5787 (mtt) REVERT: p 591 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6878 (mtm-85) REVERT: p 606 ASP cc_start: 0.6661 (t0) cc_final: 0.5916 (t0) REVERT: p 609 GLU cc_start: 0.5980 (mm-30) cc_final: 0.5497 (mt-10) REVERT: p 629 GLU cc_start: 0.7692 (tp30) cc_final: 0.7486 (tp30) REVERT: p 641 ASP cc_start: 0.7636 (m-30) cc_final: 0.6924 (m-30) REVERT: p 647 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6129 (pm20) REVERT: p 728 MET cc_start: 0.7346 (mtm) cc_final: 0.7059 (mtp) REVERT: p 745 ASP cc_start: 0.6705 (m-30) cc_final: 0.6260 (m-30) REVERT: p 761 THR cc_start: 0.8508 (m) cc_final: 0.8149 (p) REVERT: p 764 MET cc_start: 0.8173 (mtt) cc_final: 0.7798 (mtp) REVERT: p 770 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6823 (mtm-85) REVERT: p 796 MET cc_start: 0.8546 (mtm) cc_final: 0.8026 (mmm) REVERT: p 827 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6766 (mt-10) REVERT: p 840 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6277 (mpt) REVERT: p 931 ILE cc_start: 0.7736 (pt) cc_final: 0.7379 (pp) REVERT: p 942 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7446 (pttt) REVERT: p 995 GLU cc_start: 0.7598 (mt-10) cc_final: 0.6949 (pt0) REVERT: p 1022 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6991 (tp) REVERT: p 1054 MET cc_start: 0.8295 (mtm) cc_final: 0.7874 (mtm) REVERT: p 1072 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6283 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7345 (tt0) cc_final: 0.7115 (tt0) REVERT: p 1081 ASP cc_start: 0.7128 (t0) cc_final: 0.6876 (t0) REVERT: p 1114 TYR cc_start: 0.7896 (t80) cc_final: 0.7535 (t80) REVERT: p 1121 LEU cc_start: 0.8299 (mt) cc_final: 0.8090 (mm) REVERT: p 1151 MET cc_start: 0.8188 (ptm) cc_final: 0.7881 (ptm) REVERT: p 1172 MET cc_start: 0.7117 (mmt) cc_final: 0.6808 (mmt) REVERT: q 17 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7272 (tt0) REVERT: q 103 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7887 (tp) REVERT: q 109 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6474 (pm20) REVERT: q 126 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7308 (mmm-85) REVERT: q 158 GLU cc_start: 0.6493 (tt0) cc_final: 0.6072 (pt0) REVERT: q 225 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7754 (pttm) REVERT: q 240 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.6515 (mtp85) REVERT: s 49 SER cc_start: 0.8851 (t) cc_final: 0.8321 (p) REVERT: s 116 GLN cc_start: 0.7767 (tp40) cc_final: 0.7378 (tp-100) REVERT: s 133 GLN cc_start: 0.7540 (mt0) cc_final: 0.7291 (mm-40) REVERT: s 158 GLU cc_start: 0.7127 (tt0) cc_final: 0.6610 (pt0) REVERT: s 167 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6947 (mt-10) REVERT: t 80 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.5826 (mpt) REVERT: t 82 GLU cc_start: 0.8292 (pm20) cc_final: 0.7904 (pm20) REVERT: t 84 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7711 (mp0) REVERT: u 1 MET cc_start: 0.7971 (tmm) cc_final: 0.7694 (tmm) REVERT: u 16 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6180 (ptp-170) REVERT: u 101 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6408 (tt) REVERT: v 37 MET cc_start: 0.7827 (mtp) cc_final: 0.6915 (mmm) REVERT: v 48 TYR cc_start: 0.7426 (t80) cc_final: 0.7092 (t80) REVERT: v 63 THR cc_start: 0.8858 (p) cc_final: 0.8596 (t) REVERT: v 74 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7568 (tp30) REVERT: v 76 ASN cc_start: 0.7946 (m-40) cc_final: 0.7592 (m-40) REVERT: v 95 LYS cc_start: 0.7345 (tttt) cc_final: 0.7003 (ttpt) REVERT: v 100 GLU cc_start: 0.6597 (tt0) cc_final: 0.5845 (mt-10) REVERT: v 103 GLU cc_start: 0.7159 (pm20) cc_final: 0.6935 (pm20) REVERT: v 132 LEU cc_start: 0.7241 (mt) cc_final: 0.7022 (mt) REVERT: v 146 LYS cc_start: 0.6737 (tttt) cc_final: 0.6223 (tptp) REVERT: v 147 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7968 (mmmm) REVERT: w 51 SER cc_start: 0.7737 (t) cc_final: 0.7286 (p) REVERT: w 93 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7113 (tt0) REVERT: w 115 THR cc_start: 0.7331 (m) cc_final: 0.6835 (p) REVERT: x 19 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: x 58 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7186 (mtpp) REVERT: y 8 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7004 (mm-30) REVERT: y 23 LYS cc_start: 0.8265 (mttt) cc_final: 0.7710 (ttmm) REVERT: y 55 GLN cc_start: 0.7548 (mt0) cc_final: 0.6915 (mt0) REVERT: y 77 THR cc_start: 0.9052 (p) cc_final: 0.8500 (t) REVERT: y 85 GLU cc_start: 0.6888 (tt0) cc_final: 0.6597 (tt0) REVERT: y 111 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7233 (t0) REVERT: z 18 ILE cc_start: 0.8097 (mt) cc_final: 0.7865 (mp) outliers start: 162 outliers final: 96 residues processed: 656 average time/residue: 1.5725 time to fit residues: 1236.4647 Evaluate side-chains 644 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 525 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 144 VAL Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 317 MET Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 445 LYS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 681 LEU Chi-restraints excluded: chain o residue 683 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 743 ARG Chi-restraints excluded: chain o residue 782 SER Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1479 LYS Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 579 ASP Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 840 MET Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1004 ASP Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1069 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1093 CYS Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain q residue 240 ARG Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 111 THR Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 80 MET Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 4 HIS Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 71 LYS Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 147 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 55 LEU 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 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 97 GLU Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 0.5980 chunk 366 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 407 optimal weight: 1.9990 chunk 338 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 370 HIS ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN p 430 ASN p 649 ASN p 654 GLN ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 98 ASN s 108 GLN s 168 ASN ** t 72 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** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36635 Z= 0.259 Angle : 0.476 10.073 49969 Z= 0.252 Chirality : 0.040 0.169 5568 Planarity : 0.003 0.054 6099 Dihedral : 16.495 146.720 5819 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.25 % Favored : 95.60 % Rotamer: Outliers : 4.37 % Allowed : 17.87 % Favored : 77.77 % 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: 0.74 (0.13), residues: 4137 helix: 1.83 (0.14), residues: 1421 sheet: -0.01 (0.19), residues: 677 loop : -0.23 (0.14), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 679 HIS 0.006 0.001 HIS y 69 PHE 0.015 0.001 PHE o 397 TYR 0.015 0.001 TYR p 160 ARG 0.004 0.000 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 706 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 545 time to evaluate : 3.486 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: S 111 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6422 (mppt) REVERT: o 37 THR cc_start: 0.8378 (m) cc_final: 0.7683 (p) REVERT: o 66 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7403 (pt0) REVERT: o 92 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7429 (mmmm) REVERT: o 119 VAL cc_start: 0.8131 (t) cc_final: 0.7662 (m) REVERT: o 139 LYS cc_start: 0.6872 (ttmt) cc_final: 0.6462 (mmtt) REVERT: o 151 LYS cc_start: 0.7343 (mmtp) cc_final: 0.6849 (mmtm) REVERT: o 193 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8288 (tmm-80) REVERT: o 240 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8139 (Cg_exo) REVERT: o 309 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6960 (tp) REVERT: o 316 THR cc_start: 0.7161 (m) cc_final: 0.6807 (p) REVERT: o 317 MET cc_start: 0.7034 (ttp) cc_final: 0.6823 (ttt) REVERT: o 520 MET cc_start: 0.7761 (mmt) cc_final: 0.7211 (mmt) REVERT: o 524 MET cc_start: 0.8190 (mmp) cc_final: 0.7068 (mmm) REVERT: o 532 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6063 (ptp90) REVERT: o 561 MET cc_start: 0.7332 (mtt) cc_final: 0.6901 (mtt) REVERT: o 634 GLU cc_start: 0.7046 (tt0) cc_final: 0.6242 (mt-10) REVERT: o 683 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: o 700 GLN cc_start: 0.6579 (tt0) cc_final: 0.6125 (tp40) REVERT: o 711 GLN cc_start: 0.5770 (tt0) cc_final: 0.5440 (tp-100) REVERT: o 728 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6971 (t) REVERT: o 743 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5853 (ttm110) REVERT: o 796 LYS cc_start: 0.7034 (mttt) cc_final: 0.6604 (mtpp) REVERT: o 919 LYS cc_start: 0.6614 (mttt) cc_final: 0.6304 (mptp) REVERT: o 1008 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6881 (tppt) REVERT: o 1054 MET cc_start: 0.7834 (mmt) cc_final: 0.7527 (mmm) REVERT: o 1136 THR cc_start: 0.9019 (m) cc_final: 0.8780 (p) REVERT: o 1168 LYS cc_start: 0.7459 (mttt) cc_final: 0.6881 (mptt) REVERT: o 1219 LYS cc_start: 0.7962 (tppp) cc_final: 0.7650 (tppp) REVERT: o 1259 ILE cc_start: 0.6984 (mt) cc_final: 0.6571 (mm) REVERT: o 1279 MET cc_start: 0.6675 (mtm) cc_final: 0.6413 (mtt) REVERT: o 1306 LYS cc_start: 0.6772 (mttt) cc_final: 0.5912 (mmmt) REVERT: o 1321 ILE cc_start: 0.7235 (mt) cc_final: 0.6838 (pp) REVERT: o 1329 LYS cc_start: 0.7444 (tttt) cc_final: 0.7009 (tttm) REVERT: o 1332 GLN cc_start: 0.8380 (mt0) cc_final: 0.8081 (tt0) REVERT: o 1351 ASP cc_start: 0.7666 (m-30) cc_final: 0.7299 (m-30) REVERT: o 1364 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5852 (mm-30) REVERT: o 1372 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7242 (mm-30) REVERT: o 1412 MET cc_start: 0.7836 (ttp) cc_final: 0.7392 (tmm) REVERT: o 1422 GLN cc_start: 0.6710 (mt0) cc_final: 0.5931 (mm110) REVERT: p 155 MET cc_start: 0.7996 (ttm) cc_final: 0.7752 (ttm) REVERT: p 200 MET cc_start: 0.7862 (ttm) cc_final: 0.7081 (ttm) REVERT: p 239 MET cc_start: 0.6406 (ttm) cc_final: 0.6191 (ttp) REVERT: p 254 GLN cc_start: 0.5773 (mt0) cc_final: 0.5286 (mp10) REVERT: p 304 SER cc_start: 0.7331 (t) cc_final: 0.6994 (m) REVERT: p 309 PHE cc_start: 0.8477 (t80) cc_final: 0.8206 (t80) REVERT: p 386 ASP cc_start: 0.7762 (m-30) cc_final: 0.7304 (m-30) REVERT: p 471 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7443 (t0) REVERT: p 508 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.5805 (mtt) REVERT: p 561 ILE cc_start: 0.5344 (OUTLIER) cc_final: 0.5123 (mt) REVERT: p 591 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7127 (mtm-85) REVERT: p 593 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6499 (mp10) REVERT: p 606 ASP cc_start: 0.6803 (t0) cc_final: 0.6048 (t0) REVERT: p 609 GLU cc_start: 0.6320 (mm-30) cc_final: 0.5823 (mt-10) REVERT: p 629 GLU cc_start: 0.7660 (tp30) cc_final: 0.7427 (tp30) REVERT: p 641 ASP cc_start: 0.7596 (m-30) cc_final: 0.6900 (m-30) REVERT: p 647 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6691 (pm20) REVERT: p 728 MET cc_start: 0.7368 (mtm) cc_final: 0.7102 (mtp) REVERT: p 745 ASP cc_start: 0.6688 (m-30) cc_final: 0.6246 (m-30) REVERT: p 761 THR cc_start: 0.8497 (m) cc_final: 0.8136 (p) REVERT: p 764 MET cc_start: 0.8194 (mtt) cc_final: 0.7815 (mtp) REVERT: p 770 ARG cc_start: 0.7562 (mtm110) cc_final: 0.7142 (mtm-85) REVERT: p 796 MET cc_start: 0.8549 (mtm) cc_final: 0.8040 (mmm) REVERT: p 827 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6674 (mt-10) REVERT: p 863 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7565 (t0) REVERT: p 897 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7344 (mtt180) REVERT: p 931 ILE cc_start: 0.7671 (pt) cc_final: 0.7338 (pp) REVERT: p 942 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7495 (pmtt) REVERT: p 995 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6931 (pt0) REVERT: p 1022 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6933 (tp) REVERT: p 1054 MET cc_start: 0.8299 (mtm) cc_final: 0.7897 (mtm) REVERT: p 1072 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6271 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7358 (tt0) cc_final: 0.7087 (tt0) REVERT: p 1081 ASP cc_start: 0.7156 (t0) cc_final: 0.6883 (t0) REVERT: p 1109 GLU cc_start: 0.6565 (mt-10) cc_final: 0.6265 (mt-10) REVERT: p 1114 TYR cc_start: 0.7894 (t80) cc_final: 0.7576 (t80) REVERT: p 1121 LEU cc_start: 0.8299 (mt) cc_final: 0.8095 (mm) REVERT: p 1131 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7721 (ptp-170) REVERT: p 1151 MET cc_start: 0.8192 (ptm) cc_final: 0.7881 (ptm) REVERT: p 1172 MET cc_start: 0.7047 (mmt) cc_final: 0.6741 (mmt) REVERT: q 17 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7305 (tt0) REVERT: q 103 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (tp) REVERT: q 109 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6663 (pm20) REVERT: q 126 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7237 (mmm-85) REVERT: q 158 GLU cc_start: 0.6605 (tt0) cc_final: 0.6252 (pt0) REVERT: q 166 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6482 (mtmt) REVERT: q 225 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7814 (pttm) REVERT: s 49 SER cc_start: 0.8820 (t) cc_final: 0.8264 (p) REVERT: s 116 GLN cc_start: 0.7715 (tp40) cc_final: 0.7256 (tp-100) REVERT: s 133 GLN cc_start: 0.7708 (mt0) cc_final: 0.7474 (mm-40) REVERT: s 134 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7256 (mt-10) REVERT: s 158 GLU cc_start: 0.7118 (tt0) cc_final: 0.6634 (pt0) REVERT: s 167 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7020 (mt-10) REVERT: t 82 GLU cc_start: 0.8337 (pm20) cc_final: 0.8048 (pm20) REVERT: t 84 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7805 (mp0) REVERT: u 1 MET cc_start: 0.7832 (tmm) cc_final: 0.7200 (tmt) REVERT: u 16 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6226 (ptp-170) REVERT: u 101 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6374 (mp) REVERT: u 104 MET cc_start: 0.6608 (tpp) cc_final: 0.5757 (tpp) REVERT: v 20 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6535 (tptp) REVERT: v 28 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7130 (mt) REVERT: v 37 MET cc_start: 0.7820 (mtp) cc_final: 0.6918 (mmm) REVERT: v 55 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6873 (ttmt) REVERT: v 63 THR cc_start: 0.8851 (p) cc_final: 0.8579 (t) REVERT: v 74 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: v 76 ASN cc_start: 0.7938 (m-40) cc_final: 0.7565 (m-40) REVERT: v 95 LYS cc_start: 0.7053 (tttt) cc_final: 0.6724 (ttpt) REVERT: v 100 GLU cc_start: 0.6587 (tt0) cc_final: 0.5836 (mt-10) REVERT: v 103 GLU cc_start: 0.7618 (pm20) cc_final: 0.7310 (pm20) REVERT: v 132 LEU cc_start: 0.7100 (mt) cc_final: 0.6866 (mt) REVERT: v 146 LYS cc_start: 0.6719 (tttt) cc_final: 0.6193 (tptp) REVERT: v 147 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7963 (mttt) REVERT: w 18 GLN cc_start: 0.8483 (tt0) cc_final: 0.7906 (pp30) REVERT: w 47 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8275 (pp20) REVERT: w 51 SER cc_start: 0.7793 (t) cc_final: 0.7352 (p) REVERT: w 93 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7054 (tt0) REVERT: w 115 THR cc_start: 0.7265 (m) cc_final: 0.6784 (p) REVERT: x 19 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: x 58 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7232 (mtpp) REVERT: y 8 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7032 (mm-30) REVERT: y 16 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5954 (tt0) REVERT: y 23 LYS cc_start: 0.8252 (mttt) cc_final: 0.7681 (tppt) REVERT: y 55 GLN cc_start: 0.7618 (mt0) cc_final: 0.6943 (mt0) REVERT: y 68 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: y 77 THR cc_start: 0.9030 (p) cc_final: 0.8460 (t) REVERT: y 85 GLU cc_start: 0.6864 (tt0) cc_final: 0.6580 (tt0) REVERT: y 111 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7243 (t0) REVERT: z 18 ILE cc_start: 0.7962 (mt) cc_final: 0.7731 (mp) outliers start: 161 outliers final: 95 residues processed: 638 average time/residue: 1.5689 time to fit residues: 1199.9394 Evaluate side-chains 654 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 529 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain o residue 18 ILE Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 423 ASN Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 683 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 743 ARG Chi-restraints excluded: chain o residue 782 SER Chi-restraints excluded: chain o residue 847 LEU Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 1008 LYS Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1161 LEU Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 224 CYS Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 344 GLN Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 579 ASP Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 593 GLN Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 681 ASP Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 863 ASP Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 1004 ASP Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1093 CYS Chi-restraints excluded: chain p residue 1130 THR Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 70 ASP Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 VAL Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 147 ILE Chi-restraints excluded: chain v residue 20 LYS Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 138 ASP Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain v residue 147 LYS Chi-restraints excluded: chain w residue 15 ARG Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 19 GLU Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 232 optimal weight: 0.0270 chunk 297 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 342 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 405 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 330 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** o1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1332 GLN ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN p 525 ASN p 654 GLN ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 260 GLN s 98 ASN s 108 GLN s 168 ASN ** t 72 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** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36635 Z= 0.210 Angle : 0.451 10.277 49969 Z= 0.239 Chirality : 0.039 0.167 5568 Planarity : 0.003 0.051 6099 Dihedral : 16.421 145.352 5819 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.35 % Favored : 95.50 % Rotamer: Outliers : 4.12 % Allowed : 18.28 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4137 helix: 1.97 (0.14), residues: 1414 sheet: 0.01 (0.19), residues: 686 loop : -0.21 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 679 HIS 0.005 0.001 HIS y 69 PHE 0.012 0.001 PHE p 402 TYR 0.021 0.001 TYR r 67 ARG 0.004 0.000 ARG p 592 *********************** 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 691 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 539 time to evaluate : 4.085 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: S 111 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6393 (mppt) REVERT: o 37 THR cc_start: 0.8380 (m) cc_final: 0.7695 (p) REVERT: o 66 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7519 (pt0) REVERT: o 119 VAL cc_start: 0.8115 (t) cc_final: 0.7667 (m) REVERT: o 139 LYS cc_start: 0.6876 (ttmt) cc_final: 0.6472 (mmtt) REVERT: o 149 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7482 (ttpp) REVERT: o 151 LYS cc_start: 0.7490 (mmtp) cc_final: 0.7015 (mmtm) REVERT: o 193 ARG cc_start: 0.8547 (ttp80) cc_final: 0.8302 (tmm-80) REVERT: o 240 PRO cc_start: 0.8372 (Cg_endo) cc_final: 0.8093 (Cg_exo) REVERT: o 309 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6958 (tp) REVERT: o 316 THR cc_start: 0.7025 (m) cc_final: 0.6638 (p) REVERT: o 520 MET cc_start: 0.7750 (mmt) cc_final: 0.7222 (mmt) REVERT: o 524 MET cc_start: 0.8223 (mmp) cc_final: 0.7108 (mmm) REVERT: o 532 ARG cc_start: 0.6772 (mtm110) cc_final: 0.6117 (ptp90) REVERT: o 634 GLU cc_start: 0.7039 (tt0) cc_final: 0.6234 (mt-10) REVERT: o 683 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: o 700 GLN cc_start: 0.6579 (tt0) cc_final: 0.6089 (tp40) REVERT: o 711 GLN cc_start: 0.5765 (tt0) cc_final: 0.5439 (tp-100) REVERT: o 743 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5854 (ttm110) REVERT: o 796 LYS cc_start: 0.7031 (mttt) cc_final: 0.6604 (mtpp) REVERT: o 919 LYS cc_start: 0.6633 (mttt) cc_final: 0.6301 (mptp) REVERT: o 1008 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6879 (tppt) REVERT: o 1054 MET cc_start: 0.7819 (mmt) cc_final: 0.7574 (mmm) REVERT: o 1136 THR cc_start: 0.9006 (m) cc_final: 0.8759 (p) REVERT: o 1168 LYS cc_start: 0.7385 (mttt) cc_final: 0.6898 (mptt) REVERT: o 1219 LYS cc_start: 0.7977 (tppp) cc_final: 0.7655 (tppp) REVERT: o 1259 ILE cc_start: 0.7076 (mt) cc_final: 0.6658 (mm) REVERT: o 1279 MET cc_start: 0.6724 (mtm) cc_final: 0.6431 (mtt) REVERT: o 1306 LYS cc_start: 0.6639 (mttt) cc_final: 0.5810 (mmmt) REVERT: o 1321 ILE cc_start: 0.7297 (mt) cc_final: 0.6882 (pp) REVERT: o 1329 LYS cc_start: 0.7371 (tttt) cc_final: 0.6945 (tttm) REVERT: o 1332 GLN cc_start: 0.8386 (mt0) cc_final: 0.8168 (tt0) REVERT: o 1364 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5845 (mm-30) REVERT: o 1372 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7248 (mm-30) REVERT: o 1412 MET cc_start: 0.7817 (ttp) cc_final: 0.7386 (tmm) REVERT: o 1422 GLN cc_start: 0.6716 (mt0) cc_final: 0.5935 (mm110) REVERT: o 1481 LYS cc_start: 0.6679 (ttpt) cc_final: 0.6334 (ttpp) REVERT: p 144 HIS cc_start: 0.7556 (m90) cc_final: 0.7259 (m90) REVERT: p 155 MET cc_start: 0.7947 (ttm) cc_final: 0.7683 (ttm) REVERT: p 200 MET cc_start: 0.7829 (ttm) cc_final: 0.7066 (ttm) REVERT: p 239 MET cc_start: 0.6374 (ttm) cc_final: 0.6135 (ttp) REVERT: p 254 GLN cc_start: 0.5761 (mt0) cc_final: 0.5290 (mp10) REVERT: p 304 SER cc_start: 0.7420 (t) cc_final: 0.7102 (m) REVERT: p 309 PHE cc_start: 0.8463 (t80) cc_final: 0.8178 (t80) REVERT: p 344 GLN cc_start: 0.7647 (tt0) cc_final: 0.7441 (tt0) REVERT: p 386 ASP cc_start: 0.7746 (m-30) cc_final: 0.7297 (m-30) REVERT: p 471 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7404 (t0) REVERT: p 508 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.5704 (mtt) REVERT: p 516 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: p 561 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.5119 (mt) REVERT: p 591 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: p 606 ASP cc_start: 0.6782 (t0) cc_final: 0.6103 (t0) REVERT: p 609 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5828 (mt-10) REVERT: p 629 GLU cc_start: 0.7692 (tp30) cc_final: 0.7453 (tp30) REVERT: p 641 ASP cc_start: 0.7597 (m-30) cc_final: 0.6897 (m-30) REVERT: p 647 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6704 (pm20) REVERT: p 685 LYS cc_start: 0.7386 (tptt) cc_final: 0.7122 (mmmt) REVERT: p 728 MET cc_start: 0.7351 (mtm) cc_final: 0.7102 (mtp) REVERT: p 739 ASN cc_start: 0.7485 (p0) cc_final: 0.7146 (p0) REVERT: p 745 ASP cc_start: 0.6630 (m-30) cc_final: 0.6188 (m-30) REVERT: p 761 THR cc_start: 0.8489 (m) cc_final: 0.8147 (p) REVERT: p 764 MET cc_start: 0.8162 (mtt) cc_final: 0.7798 (mtp) REVERT: p 770 ARG cc_start: 0.7233 (mtm110) cc_final: 0.6930 (mtm-85) REVERT: p 796 MET cc_start: 0.8567 (mtm) cc_final: 0.8161 (mmm) REVERT: p 827 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6662 (mt-10) REVERT: p 897 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7263 (mtt180) REVERT: p 931 ILE cc_start: 0.7704 (pt) cc_final: 0.7379 (pp) REVERT: p 942 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7438 (pttt) REVERT: p 995 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6914 (pt0) REVERT: p 1022 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7162 (tp) REVERT: p 1054 MET cc_start: 0.8252 (mtm) cc_final: 0.7834 (mtm) REVERT: p 1072 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6302 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7337 (tt0) cc_final: 0.7107 (tt0) REVERT: p 1081 ASP cc_start: 0.7161 (t0) cc_final: 0.6916 (t0) REVERT: p 1114 TYR cc_start: 0.7885 (t80) cc_final: 0.7604 (t80) REVERT: p 1131 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7741 (ptp-170) REVERT: p 1151 MET cc_start: 0.8165 (ptm) cc_final: 0.7867 (ptm) REVERT: p 1172 MET cc_start: 0.6999 (mmt) cc_final: 0.6692 (mmt) REVERT: q 17 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7303 (tt0) REVERT: q 103 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7838 (tp) REVERT: q 109 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6546 (pm20) REVERT: q 126 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7298 (mmm-85) REVERT: q 158 GLU cc_start: 0.6619 (tt0) cc_final: 0.6263 (pt0) REVERT: q 166 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6456 (mtmt) REVERT: q 225 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7796 (pttm) REVERT: s 49 SER cc_start: 0.8816 (t) cc_final: 0.8242 (p) REVERT: s 116 GLN cc_start: 0.7662 (tp40) cc_final: 0.7282 (tp-100) REVERT: s 133 GLN cc_start: 0.7699 (mt0) cc_final: 0.7456 (mm-40) REVERT: s 134 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7268 (mt-10) REVERT: s 158 GLU cc_start: 0.7125 (tt0) cc_final: 0.6632 (pt0) REVERT: s 167 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7000 (mt-10) REVERT: t 82 GLU cc_start: 0.8541 (pm20) cc_final: 0.8249 (pm20) REVERT: t 84 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7835 (mp0) REVERT: u 1 MET cc_start: 0.7662 (tmm) cc_final: 0.7168 (tmt) REVERT: u 16 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6019 (ptp-170) REVERT: u 101 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6283 (mp) REVERT: u 147 ILE cc_start: 0.9292 (mp) cc_final: 0.9031 (tp) REVERT: v 20 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6527 (tptp) REVERT: v 28 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7052 (mt) REVERT: v 37 MET cc_start: 0.7851 (mtp) cc_final: 0.6934 (mmm) REVERT: v 55 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6763 (ttmt) REVERT: v 63 THR cc_start: 0.8840 (p) cc_final: 0.8570 (t) REVERT: v 74 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: v 76 ASN cc_start: 0.7941 (m-40) cc_final: 0.7566 (m-40) REVERT: v 95 LYS cc_start: 0.7262 (tttt) cc_final: 0.6993 (ttpt) REVERT: v 100 GLU cc_start: 0.6626 (tt0) cc_final: 0.5851 (mt-10) REVERT: v 103 GLU cc_start: 0.7633 (pm20) cc_final: 0.7330 (pm20) REVERT: v 132 LEU cc_start: 0.7104 (mt) cc_final: 0.6871 (mt) REVERT: v 146 LYS cc_start: 0.6716 (tttt) cc_final: 0.6196 (tptp) REVERT: v 147 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7950 (mttt) REVERT: w 18 GLN cc_start: 0.8594 (tt0) cc_final: 0.7889 (pp30) REVERT: w 47 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8277 (pp20) REVERT: w 51 SER cc_start: 0.7782 (t) cc_final: 0.7339 (p) REVERT: w 93 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7027 (tt0) REVERT: w 115 THR cc_start: 0.7238 (m) cc_final: 0.6761 (p) REVERT: x 58 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7267 (mtpp) REVERT: y 8 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7124 (mm-30) REVERT: y 23 LYS cc_start: 0.8346 (mttt) cc_final: 0.7728 (tppt) REVERT: y 55 GLN cc_start: 0.7626 (mt0) cc_final: 0.6959 (mt0) REVERT: y 68 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: y 77 THR cc_start: 0.9027 (p) cc_final: 0.8472 (t) REVERT: y 85 GLU cc_start: 0.6858 (tt0) cc_final: 0.6582 (tt0) REVERT: y 111 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7254 (t0) REVERT: z 18 ILE cc_start: 0.7955 (mt) cc_final: 0.7682 (mp) outliers start: 152 outliers final: 94 residues processed: 628 average time/residue: 1.6152 time to fit residues: 1215.3823 Evaluate side-chains 653 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 532 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain o residue 34 MET Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 191 ILE Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 681 LEU Chi-restraints excluded: chain o residue 683 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 743 ARG Chi-restraints excluded: chain o residue 782 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1008 LYS Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1169 VAL Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1282 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 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 o residue 1430 CYS Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 591 ARG Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 681 ASP Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1004 ASP Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1026 GLU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1075 MET Chi-restraints excluded: chain p residue 1093 CYS Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain p residue 1171 MET Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 174 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 105 ILE 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 76 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 20 LYS Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain v residue 147 LYS Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 14 GLU 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 68 GLU Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 0.0470 chunk 162 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 257 optimal weight: 2.9990 chunk 276 optimal weight: 0.0570 chunk 200 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN o 731 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN o1220 HIS ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN p 518 HIS ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 654 GLN ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 98 ASN s 108 GLN s 168 ASN ** t 72 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36635 Z= 0.168 Angle : 0.436 9.983 49969 Z= 0.231 Chirality : 0.039 0.167 5568 Planarity : 0.003 0.048 6099 Dihedral : 16.330 143.682 5819 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 29.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 3.88 % Allowed : 18.74 % Favored : 77.39 % 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: 0.93 (0.13), residues: 4137 helix: 2.09 (0.14), residues: 1421 sheet: 0.03 (0.19), residues: 694 loop : -0.19 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP o 679 HIS 0.006 0.001 HIS p 518 PHE 0.015 0.001 PHE o 397 TYR 0.019 0.001 TYR r 67 ARG 0.003 0.000 ARG p 770 *********************** 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 688 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 545 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 111 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6310 (mppt) REVERT: o 37 THR cc_start: 0.8383 (m) cc_final: 0.7719 (p) REVERT: o 66 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7511 (pt0) REVERT: o 119 VAL cc_start: 0.8113 (t) cc_final: 0.7689 (m) REVERT: o 139 LYS cc_start: 0.6879 (ttmt) cc_final: 0.6470 (mmtt) REVERT: o 151 LYS cc_start: 0.7487 (mmtp) cc_final: 0.7022 (mmtm) REVERT: o 193 ARG cc_start: 0.8525 (ttp80) cc_final: 0.7927 (tmt90) REVERT: o 220 ARG cc_start: 0.7266 (tpt-90) cc_final: 0.6778 (tpt90) REVERT: o 309 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6946 (tp) REVERT: o 316 THR cc_start: 0.6932 (m) cc_final: 0.6566 (p) REVERT: o 520 MET cc_start: 0.7738 (mmt) cc_final: 0.7391 (mmt) REVERT: o 524 MET cc_start: 0.8214 (mmp) cc_final: 0.7709 (mmp) REVERT: o 561 MET cc_start: 0.7316 (mtt) cc_final: 0.6860 (mtt) REVERT: o 634 GLU cc_start: 0.7028 (tt0) cc_final: 0.6227 (mt-10) REVERT: o 683 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: o 700 GLN cc_start: 0.6567 (tt0) cc_final: 0.6055 (tp40) REVERT: o 711 GLN cc_start: 0.5755 (tt0) cc_final: 0.5432 (tp-100) REVERT: o 796 LYS cc_start: 0.7018 (mttt) cc_final: 0.6595 (mtpp) REVERT: o 919 LYS cc_start: 0.6637 (mttt) cc_final: 0.6306 (mptp) REVERT: o 1008 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6897 (tppt) REVERT: o 1054 MET cc_start: 0.7811 (mmt) cc_final: 0.7569 (mmm) REVERT: o 1136 THR cc_start: 0.8998 (m) cc_final: 0.8754 (p) REVERT: o 1146 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7788 (tp40) REVERT: o 1168 LYS cc_start: 0.7385 (mttt) cc_final: 0.6900 (mptt) REVERT: o 1219 LYS cc_start: 0.7978 (tppp) cc_final: 0.7652 (tppp) REVERT: o 1259 ILE cc_start: 0.7104 (mt) cc_final: 0.6670 (mm) REVERT: o 1279 MET cc_start: 0.6885 (mtm) cc_final: 0.6634 (mtt) REVERT: o 1306 LYS cc_start: 0.6599 (mttt) cc_final: 0.5777 (mmmt) REVERT: o 1321 ILE cc_start: 0.7414 (mt) cc_final: 0.6981 (pp) REVERT: o 1329 LYS cc_start: 0.7382 (tttt) cc_final: 0.6921 (tttm) REVERT: o 1364 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5840 (mm-30) REVERT: o 1372 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7177 (mm-30) REVERT: o 1412 MET cc_start: 0.7801 (ttp) cc_final: 0.7368 (tmm) REVERT: o 1422 GLN cc_start: 0.6774 (mt0) cc_final: 0.6017 (mm110) REVERT: o 1481 LYS cc_start: 0.6677 (ttpt) cc_final: 0.6356 (ttpp) REVERT: p 144 HIS cc_start: 0.7543 (m90) cc_final: 0.7252 (m90) REVERT: p 155 MET cc_start: 0.7940 (ttm) cc_final: 0.7684 (ttm) REVERT: p 200 MET cc_start: 0.7802 (ttm) cc_final: 0.7034 (ttm) REVERT: p 254 GLN cc_start: 0.5761 (mt0) cc_final: 0.5346 (mp10) REVERT: p 304 SER cc_start: 0.7397 (t) cc_final: 0.7108 (m) REVERT: p 309 PHE cc_start: 0.8451 (t80) cc_final: 0.8199 (t80) REVERT: p 344 GLN cc_start: 0.7638 (tt0) cc_final: 0.7408 (tt0) REVERT: p 386 ASP cc_start: 0.7734 (m-30) cc_final: 0.7300 (m-30) REVERT: p 471 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7372 (t0) REVERT: p 508 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.5708 (mtt) REVERT: p 561 ILE cc_start: 0.5289 (OUTLIER) cc_final: 0.5068 (mt) REVERT: p 593 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6505 (mp10) REVERT: p 606 ASP cc_start: 0.6774 (t0) cc_final: 0.6133 (t0) REVERT: p 609 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5911 (mt-10) REVERT: p 629 GLU cc_start: 0.7744 (tp30) cc_final: 0.7526 (tp30) REVERT: p 641 ASP cc_start: 0.7599 (m-30) cc_final: 0.6895 (m-30) REVERT: p 647 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6415 (pm20) REVERT: p 685 LYS cc_start: 0.7497 (tptt) cc_final: 0.7175 (mmmt) REVERT: p 728 MET cc_start: 0.7338 (mtm) cc_final: 0.7111 (mtp) REVERT: p 761 THR cc_start: 0.8478 (m) cc_final: 0.8152 (p) REVERT: p 764 MET cc_start: 0.8168 (mtt) cc_final: 0.7761 (mtp) REVERT: p 770 ARG cc_start: 0.7208 (mtm110) cc_final: 0.6906 (mtm-85) REVERT: p 796 MET cc_start: 0.8544 (mtm) cc_final: 0.8097 (mmm) REVERT: p 827 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6717 (mt-10) REVERT: p 942 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7496 (pttt) REVERT: p 995 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6882 (pt0) REVERT: p 1022 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7091 (tp) REVERT: p 1054 MET cc_start: 0.8226 (mtm) cc_final: 0.7903 (mtm) REVERT: p 1072 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6289 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7347 (tt0) cc_final: 0.7097 (tt0) REVERT: p 1081 ASP cc_start: 0.7078 (t0) cc_final: 0.6859 (t0) REVERT: p 1109 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6401 (mt-10) REVERT: p 1114 TYR cc_start: 0.7798 (t80) cc_final: 0.7543 (t80) REVERT: p 1131 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7600 (ptp-170) REVERT: p 1151 MET cc_start: 0.8168 (ptm) cc_final: 0.7868 (ptm) REVERT: p 1172 MET cc_start: 0.6978 (mmt) cc_final: 0.6671 (mmt) REVERT: q 17 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7269 (tt0) REVERT: q 103 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7801 (tp) REVERT: q 109 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6522 (pm20) REVERT: q 126 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7302 (mmm-85) REVERT: q 158 GLU cc_start: 0.6758 (tt0) cc_final: 0.6342 (pt0) REVERT: q 166 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6435 (mtmt) REVERT: q 225 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7722 (pttm) REVERT: s 49 SER cc_start: 0.8796 (t) cc_final: 0.8212 (p) REVERT: s 88 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8182 (mmmt) REVERT: s 116 GLN cc_start: 0.7600 (tp40) cc_final: 0.7265 (tp-100) REVERT: s 133 GLN cc_start: 0.7645 (mt0) cc_final: 0.7422 (mm-40) REVERT: s 134 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7243 (mt-10) REVERT: s 158 GLU cc_start: 0.7132 (tt0) cc_final: 0.6633 (pt0) REVERT: s 167 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6976 (mt-10) REVERT: t 82 GLU cc_start: 0.8588 (pm20) cc_final: 0.8255 (pm20) REVERT: t 84 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7869 (mp0) REVERT: u 1 MET cc_start: 0.7654 (tmm) cc_final: 0.7172 (tmt) REVERT: u 101 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6287 (mp) REVERT: u 104 MET cc_start: 0.5968 (tpp) cc_final: 0.5158 (tpp) REVERT: v 20 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6648 (tptp) REVERT: v 28 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7019 (mt) REVERT: v 37 MET cc_start: 0.7815 (mtp) cc_final: 0.6923 (mmm) REVERT: v 55 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6698 (ttmt) REVERT: v 63 THR cc_start: 0.8839 (p) cc_final: 0.8565 (t) REVERT: v 74 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: v 76 ASN cc_start: 0.7909 (m-40) cc_final: 0.7520 (m-40) REVERT: v 95 LYS cc_start: 0.7265 (tttt) cc_final: 0.7015 (ttpt) REVERT: v 100 GLU cc_start: 0.6639 (tt0) cc_final: 0.5857 (mt-10) REVERT: v 103 GLU cc_start: 0.7648 (pm20) cc_final: 0.7238 (pm20) REVERT: v 132 LEU cc_start: 0.7093 (mt) cc_final: 0.6872 (mt) REVERT: v 141 VAL cc_start: 0.7243 (OUTLIER) cc_final: 0.6989 (p) REVERT: v 146 LYS cc_start: 0.6728 (tttt) cc_final: 0.6197 (tptp) REVERT: v 147 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7936 (mttt) REVERT: w 18 GLN cc_start: 0.8594 (tt0) cc_final: 0.7881 (pp30) REVERT: w 47 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8266 (pp20) REVERT: w 51 SER cc_start: 0.7777 (t) cc_final: 0.7336 (p) REVERT: w 93 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7018 (tt0) REVERT: w 115 THR cc_start: 0.7190 (m) cc_final: 0.6707 (p) REVERT: x 58 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7347 (mtpp) REVERT: y 8 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7081 (mm-30) REVERT: y 16 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5970 (tt0) REVERT: y 23 LYS cc_start: 0.8324 (mttt) cc_final: 0.7776 (tppt) REVERT: y 55 GLN cc_start: 0.7629 (mt0) cc_final: 0.6915 (mt0) REVERT: y 68 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: y 77 THR cc_start: 0.9045 (p) cc_final: 0.8503 (t) REVERT: y 85 GLU cc_start: 0.6835 (tt0) cc_final: 0.6567 (tt0) REVERT: y 93 ASP cc_start: 0.7388 (m-30) cc_final: 0.7187 (m-30) REVERT: y 111 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7268 (t0) outliers start: 143 outliers final: 93 residues processed: 628 average time/residue: 1.5937 time to fit residues: 1199.9058 Evaluate side-chains 650 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 529 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 336 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 681 LEU Chi-restraints excluded: chain o residue 683 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 782 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1008 LYS Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1161 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1282 ASP Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 579 ASP Chi-restraints excluded: chain p residue 593 GLN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1026 GLU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1130 THR Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain p residue 1171 MET Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 68 LEU Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 88 LYS Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 111 THR Chi-restraints excluded: chain s residue 174 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 VAL Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 147 ILE Chi-restraints excluded: chain v residue 20 LYS Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 138 ASP Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain v residue 147 LYS Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 55 LEU Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 16 GLU Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 27 VAL Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain y residue 97 GLU Chi-restraints excluded: chain y residue 111 ASP Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 354 optimal weight: 0.1980 chunk 378 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 296 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 0.6980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN o 791 GLN ** o 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS o1332 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN p 518 HIS p 654 GLN ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS s 98 ASN s 108 GLN s 168 ASN ** t 72 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 36635 Z= 0.353 Angle : 0.520 10.831 49969 Z= 0.273 Chirality : 0.042 0.174 5568 Planarity : 0.004 0.056 6099 Dihedral : 16.336 141.435 5819 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 29.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.14 % Rotamer: Outliers : 3.93 % Allowed : 18.95 % Favored : 77.11 % 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: 0.65 (0.13), residues: 4137 helix: 1.80 (0.14), residues: 1411 sheet: -0.04 (0.19), residues: 691 loop : -0.33 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 49 HIS 0.008 0.001 HIS y 69 PHE 0.014 0.001 PHE q 63 TYR 0.023 0.002 TYR r 67 ARG 0.006 0.000 ARG o 805 *********************** 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 673 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 528 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 111 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6433 (mppt) REVERT: o 37 THR cc_start: 0.8470 (m) cc_final: 0.7792 (p) REVERT: o 66 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7535 (pt0) REVERT: o 119 VAL cc_start: 0.8110 (t) cc_final: 0.7691 (m) REVERT: o 139 LYS cc_start: 0.6901 (ttmt) cc_final: 0.6493 (mmtt) REVERT: o 151 LYS cc_start: 0.7512 (mmtp) cc_final: 0.7059 (mmtm) REVERT: o 193 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8290 (tmm-80) REVERT: o 309 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6991 (tp) REVERT: o 316 THR cc_start: 0.6895 (m) cc_final: 0.6469 (p) REVERT: o 520 MET cc_start: 0.7781 (mmt) cc_final: 0.7218 (mmt) REVERT: o 524 MET cc_start: 0.8228 (mmp) cc_final: 0.7088 (mmm) REVERT: o 634 GLU cc_start: 0.6984 (tt0) cc_final: 0.6073 (mt-10) REVERT: o 683 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: o 700 GLN cc_start: 0.6587 (tt0) cc_final: 0.6107 (tp40) REVERT: o 711 GLN cc_start: 0.5780 (tt0) cc_final: 0.5451 (tp-100) REVERT: o 743 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.5863 (ttm110) REVERT: o 775 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7143 (mmtp) REVERT: o 796 LYS cc_start: 0.7074 (mttt) cc_final: 0.6614 (mtpp) REVERT: o 919 LYS cc_start: 0.6634 (mttt) cc_final: 0.6267 (mptp) REVERT: o 1008 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6945 (tppt) REVERT: o 1054 MET cc_start: 0.7856 (mmt) cc_final: 0.7592 (mmm) REVERT: o 1136 THR cc_start: 0.9083 (m) cc_final: 0.8808 (p) REVERT: o 1146 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7633 (tp40) REVERT: o 1168 LYS cc_start: 0.7414 (mttt) cc_final: 0.6928 (mptt) REVERT: o 1219 LYS cc_start: 0.8021 (tppp) cc_final: 0.7701 (tppp) REVERT: o 1259 ILE cc_start: 0.7103 (mt) cc_final: 0.6689 (mm) REVERT: o 1306 LYS cc_start: 0.6601 (mttt) cc_final: 0.5779 (mmmt) REVERT: o 1321 ILE cc_start: 0.7388 (mt) cc_final: 0.6929 (pp) REVERT: o 1329 LYS cc_start: 0.7339 (tttt) cc_final: 0.6892 (tttm) REVERT: o 1364 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5880 (mm-30) REVERT: o 1372 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7327 (mm-30) REVERT: o 1412 MET cc_start: 0.7833 (ttp) cc_final: 0.7346 (tmm) REVERT: o 1422 GLN cc_start: 0.6766 (mt0) cc_final: 0.5992 (mm110) REVERT: o 1481 LYS cc_start: 0.6802 (ttpt) cc_final: 0.6504 (pttp) REVERT: p 155 MET cc_start: 0.8011 (ttm) cc_final: 0.7807 (ttm) REVERT: p 200 MET cc_start: 0.7796 (ttm) cc_final: 0.7050 (ttm) REVERT: p 254 GLN cc_start: 0.5586 (mt0) cc_final: 0.5296 (mp10) REVERT: p 292 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7101 (m-10) REVERT: p 304 SER cc_start: 0.7434 (t) cc_final: 0.7139 (m) REVERT: p 309 PHE cc_start: 0.8466 (t80) cc_final: 0.8243 (t80) REVERT: p 386 ASP cc_start: 0.7746 (m-30) cc_final: 0.7278 (m-30) REVERT: p 471 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7373 (t0) REVERT: p 508 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.5762 (mtt) REVERT: p 561 ILE cc_start: 0.5402 (OUTLIER) cc_final: 0.5180 (mt) REVERT: p 579 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6171 (p0) REVERT: p 593 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6508 (mp10) REVERT: p 606 ASP cc_start: 0.6818 (t0) cc_final: 0.6155 (t0) REVERT: p 609 GLU cc_start: 0.6179 (mm-30) cc_final: 0.5908 (mt-10) REVERT: p 641 ASP cc_start: 0.7503 (m-30) cc_final: 0.6833 (m-30) REVERT: p 647 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6730 (pm20) REVERT: p 685 LYS cc_start: 0.7370 (tptt) cc_final: 0.7141 (mmmt) REVERT: p 728 MET cc_start: 0.7458 (mtm) cc_final: 0.7227 (mtp) REVERT: p 745 ASP cc_start: 0.6733 (m-30) cc_final: 0.6297 (m-30) REVERT: p 761 THR cc_start: 0.8506 (m) cc_final: 0.8168 (p) REVERT: p 770 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7216 (mtm-85) REVERT: p 796 MET cc_start: 0.8598 (mtm) cc_final: 0.8077 (mmm) REVERT: p 827 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6563 (mt-10) REVERT: p 931 ILE cc_start: 0.7797 (pt) cc_final: 0.7447 (pp) REVERT: p 942 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7543 (pmtt) REVERT: p 995 GLU cc_start: 0.7656 (mt-10) cc_final: 0.6987 (pt0) REVERT: p 1022 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7031 (tp) REVERT: p 1054 MET cc_start: 0.8315 (mtm) cc_final: 0.7920 (mtm) REVERT: p 1072 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6341 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7351 (tt0) cc_final: 0.7112 (tt0) REVERT: p 1081 ASP cc_start: 0.7294 (t0) cc_final: 0.7072 (t0) REVERT: p 1114 TYR cc_start: 0.7858 (t80) cc_final: 0.7608 (t80) REVERT: p 1151 MET cc_start: 0.8183 (ptm) cc_final: 0.7882 (ptm) REVERT: q 17 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7201 (tt0) REVERT: q 103 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7924 (tp) REVERT: q 109 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6602 (pm20) REVERT: q 126 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7296 (mmm-85) REVERT: q 158 GLU cc_start: 0.6760 (tt0) cc_final: 0.6307 (pt0) REVERT: q 166 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6554 (mtmt) REVERT: q 225 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7669 (pttm) REVERT: s 49 SER cc_start: 0.8791 (t) cc_final: 0.8199 (p) REVERT: s 88 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8229 (mmmt) REVERT: s 116 GLN cc_start: 0.7593 (tp40) cc_final: 0.7318 (tp-100) REVERT: s 133 GLN cc_start: 0.7716 (mt0) cc_final: 0.7491 (mm-40) REVERT: s 134 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7259 (mt-10) REVERT: s 158 GLU cc_start: 0.7100 (tt0) cc_final: 0.6634 (pt0) REVERT: s 167 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7001 (mt-10) REVERT: t 81 VAL cc_start: 0.7641 (t) cc_final: 0.7242 (m) REVERT: t 84 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8023 (mp0) REVERT: u 1 MET cc_start: 0.7551 (tmm) cc_final: 0.7113 (tmt) REVERT: u 16 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6015 (ptp-170) REVERT: u 101 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6367 (mp) REVERT: u 147 ILE cc_start: 0.9272 (mp) cc_final: 0.9002 (tp) REVERT: v 20 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6506 (tptp) REVERT: v 28 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7117 (mt) REVERT: v 37 MET cc_start: 0.7838 (mtp) cc_final: 0.6976 (mmm) REVERT: v 48 TYR cc_start: 0.7284 (t80) cc_final: 0.6913 (t80) REVERT: v 55 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6812 (ttmt) REVERT: v 74 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: v 76 ASN cc_start: 0.7981 (m-40) cc_final: 0.7590 (m-40) REVERT: v 95 LYS cc_start: 0.7047 (tttt) cc_final: 0.6737 (ttpt) REVERT: v 100 GLU cc_start: 0.6847 (tt0) cc_final: 0.6026 (mt-10) REVERT: v 146 LYS cc_start: 0.6711 (tttt) cc_final: 0.6169 (tptp) REVERT: v 147 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8011 (mttt) REVERT: w 18 GLN cc_start: 0.8609 (tt0) cc_final: 0.7871 (pp30) REVERT: w 46 GLN cc_start: 0.7815 (tt0) cc_final: 0.7533 (tt0) REVERT: w 47 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8204 (pp20) REVERT: w 51 SER cc_start: 0.7770 (t) cc_final: 0.7356 (p) REVERT: w 93 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7058 (tt0) REVERT: w 115 THR cc_start: 0.7225 (m) cc_final: 0.6756 (p) REVERT: x 58 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7207 (mttp) REVERT: y 8 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7107 (mm-30) REVERT: y 23 LYS cc_start: 0.8226 (mttt) cc_final: 0.7739 (tppt) REVERT: y 55 GLN cc_start: 0.7624 (mt0) cc_final: 0.7006 (mt0) REVERT: y 68 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: y 77 THR cc_start: 0.8958 (p) cc_final: 0.8384 (t) REVERT: y 85 GLU cc_start: 0.6911 (tt0) cc_final: 0.6654 (tt0) REVERT: y 111 ASP cc_start: 0.7622 (m-30) cc_final: 0.7309 (t0) outliers start: 145 outliers final: 99 residues processed: 621 average time/residue: 1.5901 time to fit residues: 1177.2344 Evaluate side-chains 644 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 517 time to evaluate : 3.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 111 LYS Chi-restraints excluded: chain o residue 35 SER Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 681 LEU Chi-restraints excluded: chain o residue 683 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 743 ARG Chi-restraints excluded: chain o residue 775 LYS Chi-restraints excluded: chain o residue 782 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 865 ILE Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1008 LYS Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1027 ASP Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1169 VAL 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 1263 ASN Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 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 o residue 1430 CYS Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 292 PHE Chi-restraints excluded: chain p residue 313 GLU Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 579 ASP Chi-restraints excluded: chain p residue 593 GLN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 710 ILE Chi-restraints excluded: chain p residue 747 LEU Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1026 GLU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1075 MET Chi-restraints excluded: chain p residue 1093 CYS Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain p residue 1171 MET Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 69 THR Chi-restraints excluded: chain s residue 88 LYS Chi-restraints excluded: chain s residue 89 VAL Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 111 THR Chi-restraints excluded: chain s residue 174 GLN Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 79 VAL Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 66 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain v residue 20 LYS Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 74 GLU Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 138 ASP Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 56 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 68 GLU Chi-restraints excluded: chain y residue 96 SER Chi-restraints excluded: chain z residue 28 ILE Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.3980 chunk 399 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 277 optimal weight: 0.2980 chunk 419 optimal weight: 0.0040 chunk 386 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN o1146 GLN o1220 HIS ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN p 518 HIS ** p 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 98 ASN s 108 GLN s 168 ASN ** t 72 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36635 Z= 0.160 Angle : 0.435 9.971 49969 Z= 0.232 Chirality : 0.039 0.167 5568 Planarity : 0.003 0.048 6099 Dihedral : 16.227 139.249 5819 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % Rotamer: Outliers : 3.20 % Allowed : 19.96 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 4137 helix: 2.08 (0.14), residues: 1413 sheet: -0.01 (0.19), residues: 694 loop : -0.25 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP o 679 HIS 0.006 0.001 HIS r 43 PHE 0.011 0.001 PHE o 397 TYR 0.021 0.001 TYR r 67 ARG 0.003 0.000 ARG p 770 ********************** 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 652 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 534 time to evaluate : 4.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 111 LYS cc_start: 0.7441 (mmmt) cc_final: 0.6401 (mppt) REVERT: o 37 THR cc_start: 0.8361 (m) cc_final: 0.7708 (p) REVERT: o 66 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7598 (pt0) REVERT: o 119 VAL cc_start: 0.8131 (t) cc_final: 0.7720 (m) REVERT: o 139 LYS cc_start: 0.6879 (ttmt) cc_final: 0.6477 (mmtt) REVERT: o 151 LYS cc_start: 0.7500 (mmtp) cc_final: 0.7063 (mmtm) REVERT: o 193 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8329 (tmm-80) REVERT: o 289 GLN cc_start: 0.6215 (tt0) cc_final: 0.5708 (tm-30) REVERT: o 309 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6968 (tp) REVERT: o 316 THR cc_start: 0.6876 (m) cc_final: 0.6508 (p) REVERT: o 520 MET cc_start: 0.7751 (mmt) cc_final: 0.7357 (mmt) REVERT: o 524 MET cc_start: 0.8247 (mmp) cc_final: 0.7706 (mmp) REVERT: o 561 MET cc_start: 0.7438 (mtt) cc_final: 0.6952 (mtt) REVERT: o 634 GLU cc_start: 0.6977 (tt0) cc_final: 0.6070 (mt-10) REVERT: o 683 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: o 700 GLN cc_start: 0.6827 (tt0) cc_final: 0.6312 (tp40) REVERT: o 711 GLN cc_start: 0.5755 (tt0) cc_final: 0.5425 (tp-100) REVERT: o 796 LYS cc_start: 0.7224 (mttt) cc_final: 0.6789 (mtpp) REVERT: o 919 LYS cc_start: 0.6671 (mttt) cc_final: 0.6317 (mptp) REVERT: o 1008 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6892 (tppt) REVERT: o 1054 MET cc_start: 0.7828 (mmt) cc_final: 0.7519 (mmm) REVERT: o 1136 THR cc_start: 0.8995 (m) cc_final: 0.8743 (p) REVERT: o 1146 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8132 (tp40) REVERT: o 1168 LYS cc_start: 0.7416 (mttt) cc_final: 0.6941 (mptt) REVERT: o 1219 LYS cc_start: 0.8023 (tppp) cc_final: 0.7708 (tppp) REVERT: o 1244 ASN cc_start: 0.6379 (t0) cc_final: 0.6004 (m-40) REVERT: o 1259 ILE cc_start: 0.7049 (mt) cc_final: 0.6627 (mm) REVERT: o 1306 LYS cc_start: 0.6625 (mttt) cc_final: 0.5814 (mmmt) REVERT: o 1321 ILE cc_start: 0.7436 (mt) cc_final: 0.6984 (pp) REVERT: o 1329 LYS cc_start: 0.7356 (tttt) cc_final: 0.6883 (tttm) REVERT: o 1364 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5843 (mm-30) REVERT: o 1372 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7190 (mm-30) REVERT: o 1379 GLU cc_start: 0.6145 (tt0) cc_final: 0.5913 (tt0) REVERT: o 1412 MET cc_start: 0.7774 (ttp) cc_final: 0.7308 (tmm) REVERT: o 1422 GLN cc_start: 0.6754 (mt0) cc_final: 0.5996 (mm110) REVERT: o 1481 LYS cc_start: 0.6726 (ttpt) cc_final: 0.6463 (pttp) REVERT: p 59 VAL cc_start: 0.6569 (OUTLIER) cc_final: 0.6102 (p) REVERT: p 144 HIS cc_start: 0.7486 (m90) cc_final: 0.7185 (m90) REVERT: p 200 MET cc_start: 0.7784 (ttm) cc_final: 0.7017 (ttm) REVERT: p 254 GLN cc_start: 0.5670 (mt0) cc_final: 0.5342 (mp10) REVERT: p 304 SER cc_start: 0.7497 (t) cc_final: 0.7231 (m) REVERT: p 309 PHE cc_start: 0.8401 (t80) cc_final: 0.8197 (t80) REVERT: p 344 GLN cc_start: 0.7563 (tt0) cc_final: 0.7211 (tp40) REVERT: p 386 ASP cc_start: 0.7713 (m-30) cc_final: 0.7264 (m-30) REVERT: p 471 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7364 (t0) REVERT: p 508 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.5684 (mtt) REVERT: p 561 ILE cc_start: 0.5294 (OUTLIER) cc_final: 0.5075 (mt) REVERT: p 593 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6443 (mp10) REVERT: p 606 ASP cc_start: 0.6770 (t0) cc_final: 0.6245 (t0) REVERT: p 609 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5935 (mt-10) REVERT: p 641 ASP cc_start: 0.7454 (m-30) cc_final: 0.6768 (m-30) REVERT: p 647 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: p 685 LYS cc_start: 0.7550 (tptt) cc_final: 0.7244 (mmmt) REVERT: p 728 MET cc_start: 0.7329 (mtm) cc_final: 0.7115 (mtp) REVERT: p 745 ASP cc_start: 0.6611 (m-30) cc_final: 0.6381 (t0) REVERT: p 761 THR cc_start: 0.8390 (m) cc_final: 0.8039 (p) REVERT: p 770 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6924 (mtm-85) REVERT: p 796 MET cc_start: 0.8583 (mtm) cc_final: 0.8127 (mmm) REVERT: p 827 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6704 (mt-10) REVERT: p 890 ARG cc_start: 0.6390 (mmm-85) cc_final: 0.6143 (mmm-85) REVERT: p 942 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7434 (pttt) REVERT: p 995 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6890 (pt0) REVERT: p 1022 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7153 (tp) REVERT: p 1054 MET cc_start: 0.8225 (mtm) cc_final: 0.7797 (mtm) REVERT: p 1072 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6301 (mtt-85) REVERT: p 1076 GLU cc_start: 0.7379 (tt0) cc_final: 0.7127 (tt0) REVERT: p 1081 ASP cc_start: 0.7231 (t0) cc_final: 0.7009 (t0) REVERT: p 1114 TYR cc_start: 0.7810 (t80) cc_final: 0.7540 (t80) REVERT: p 1131 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7660 (ptp-170) REVERT: p 1151 MET cc_start: 0.8147 (ptm) cc_final: 0.7855 (ptm) REVERT: p 1165 MET cc_start: 0.7920 (mtm) cc_final: 0.7541 (mtp) REVERT: q 17 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7307 (tt0) REVERT: q 103 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7805 (tp) REVERT: q 109 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6626 (pm20) REVERT: q 126 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7299 (mmm-85) REVERT: q 158 GLU cc_start: 0.6759 (tt0) cc_final: 0.6317 (pt0) REVERT: q 166 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6466 (mtmt) REVERT: q 225 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7724 (pttm) REVERT: s 49 SER cc_start: 0.8777 (t) cc_final: 0.8183 (p) REVERT: s 88 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8250 (mmmt) REVERT: s 116 GLN cc_start: 0.7564 (tp40) cc_final: 0.7320 (tp-100) REVERT: s 133 GLN cc_start: 0.7671 (mt0) cc_final: 0.7451 (mm-40) REVERT: s 158 GLU cc_start: 0.7049 (tt0) cc_final: 0.6577 (pt0) REVERT: s 167 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6969 (mt-10) REVERT: t 81 VAL cc_start: 0.7641 (t) cc_final: 0.7440 (p) REVERT: t 84 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7986 (mp0) REVERT: u 1 MET cc_start: 0.7521 (tmm) cc_final: 0.7080 (tmt) REVERT: u 16 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6108 (ptp-170) REVERT: u 101 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6191 (mp) REVERT: u 104 MET cc_start: 0.6228 (tpp) cc_final: 0.5507 (tpp) REVERT: v 20 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6883 (tptp) REVERT: v 28 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6997 (mt) REVERT: v 37 MET cc_start: 0.7806 (mtp) cc_final: 0.7316 (mtp) REVERT: v 55 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6571 (ttmt) REVERT: v 63 THR cc_start: 0.8880 (p) cc_final: 0.8572 (t) REVERT: v 76 ASN cc_start: 0.8050 (m-40) cc_final: 0.7682 (m-40) REVERT: v 95 LYS cc_start: 0.7259 (tttt) cc_final: 0.7012 (ttpt) REVERT: v 100 GLU cc_start: 0.6868 (tt0) cc_final: 0.6021 (mt-10) REVERT: v 103 GLU cc_start: 0.7184 (pm20) cc_final: 0.6759 (pm20) REVERT: v 141 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6968 (p) REVERT: v 146 LYS cc_start: 0.6729 (tttt) cc_final: 0.6201 (tptp) REVERT: v 147 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7922 (mttt) REVERT: w 18 GLN cc_start: 0.8532 (tt0) cc_final: 0.7810 (pp30) REVERT: w 46 GLN cc_start: 0.7826 (tt0) cc_final: 0.7530 (tt0) REVERT: w 47 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8233 (pp20) REVERT: w 51 SER cc_start: 0.7838 (t) cc_final: 0.7418 (p) REVERT: w 93 GLU cc_start: 0.7683 (mt-10) cc_final: 0.6958 (tt0) REVERT: w 115 THR cc_start: 0.7198 (m) cc_final: 0.6722 (p) REVERT: x 58 LYS cc_start: 0.7514 (mmtt) cc_final: 0.7164 (mttp) REVERT: y 8 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7053 (mm-30) REVERT: y 16 GLU cc_start: 0.6464 (tt0) cc_final: 0.5980 (tt0) REVERT: y 23 LYS cc_start: 0.8242 (mttt) cc_final: 0.7764 (tppt) REVERT: y 55 GLN cc_start: 0.7636 (mt0) cc_final: 0.6915 (mt0) REVERT: y 77 THR cc_start: 0.9034 (p) cc_final: 0.8486 (t) REVERT: y 85 GLU cc_start: 0.6836 (tt0) cc_final: 0.6591 (tt0) REVERT: y 111 ASP cc_start: 0.7621 (m-30) cc_final: 0.7322 (t0) outliers start: 118 outliers final: 78 residues processed: 606 average time/residue: 1.6642 time to fit residues: 1204.2270 Evaluate side-chains 631 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 530 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 144 VAL Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 463 THR Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 683 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 782 SER Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 1007 ILE Chi-restraints excluded: chain o residue 1008 LYS Chi-restraints excluded: chain o residue 1015 GLU Chi-restraints excluded: chain o residue 1027 ASP Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1146 GLN Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1364 GLU Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1396 ARG Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 39 LEU Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 218 THR Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 353 VAL Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 439 ILE Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 508 MET Chi-restraints excluded: chain p residue 520 VAL Chi-restraints excluded: chain p residue 561 ILE Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 579 ASP Chi-restraints excluded: chain p residue 593 GLN Chi-restraints excluded: chain p residue 596 ILE Chi-restraints excluded: chain p residue 647 GLU Chi-restraints excluded: chain p residue 894 THR Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 957 THR Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1022 LEU Chi-restraints excluded: chain p residue 1026 GLU Chi-restraints excluded: chain p residue 1067 ILE Chi-restraints excluded: chain p residue 1071 ASN Chi-restraints excluded: chain p residue 1072 ARG Chi-restraints excluded: chain p residue 1136 GLU Chi-restraints excluded: chain p residue 1171 MET Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 78 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 103 LEU Chi-restraints excluded: chain q residue 112 THR Chi-restraints excluded: chain q residue 166 LYS Chi-restraints excluded: chain q residue 207 GLU Chi-restraints excluded: chain q residue 215 GLU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 88 LYS Chi-restraints excluded: chain s residue 100 THR Chi-restraints excluded: chain s residue 111 THR Chi-restraints excluded: chain s residue 174 GLN Chi-restraints excluded: chain t residue 83 LEU Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 91 LEU Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 101 ILE Chi-restraints excluded: chain u residue 131 MET Chi-restraints excluded: chain u residue 147 ILE Chi-restraints excluded: chain v residue 20 LYS Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 138 ASP Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 82 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 y residue 96 SER Chi-restraints excluded: chain z residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 5.9990 chunk 355 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 723 ASN ** o 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o1146 GLN ** o1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 420 GLN p 518 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 265 HIS s 98 ASN s 108 GLN s 168 ASN ** t 72 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.174083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108997 restraints weight = 43018.019| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.49 r_work: 0.3189 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36635 Z= 0.276 Angle : 0.479 10.377 49969 Z= 0.252 Chirality : 0.040 0.172 5568 Planarity : 0.003 0.053 6099 Dihedral : 16.203 136.847 5819 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 29.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.50 % Favored : 95.31 % Rotamer: Outliers : 3.28 % Allowed : 19.90 % Favored : 76.82 % 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: 0.77 (0.13), residues: 4137 helix: 1.97 (0.14), residues: 1409 sheet: 0.03 (0.19), residues: 683 loop : -0.31 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 143 HIS 0.007 0.001 HIS y 69 PHE 0.012 0.001 PHE p 402 TYR 0.025 0.001 TYR r 67 ARG 0.006 0.000 ARG p 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18678.18 seconds wall clock time: 328 minutes 57.46 seconds (19737.46 seconds total)