Starting phenix.real_space_refine on Sat Mar 23 05:41:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8way_37409/03_2024/8way_37409_trim_updated.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.102 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 22168 2.51 5 N 6280 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 PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 206": "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: 0.11s 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: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 874 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "Y" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1117 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 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 71 113.947 112.510 115.216 1.00141.57 S ATOM 4763 SG CYS o 74 111.725 115.462 115.179 1.00137.29 S ATOM 4810 SG CYS o 81 110.246 111.874 114.945 1.00138.71 S ATOM 5045 SG CYS o 111 101.581 111.259 68.358 1.00164.45 S ATOM 5073 SG CYS o 114 103.743 114.595 68.040 1.00163.67 S ATOM 5419 SG CYS o 184 103.753 112.001 65.284 1.00171.81 S ATOM 24506 SG CYS p1119 105.492 125.023 104.055 1.00141.59 S ATOM 24528 SG CYS p1122 105.449 121.829 101.895 1.00142.57 S ATOM 24643 SG CYS p1137 108.306 122.481 104.022 1.00148.67 S ATOM 24664 SG CYS p1140 107.799 124.361 100.782 1.00152.98 S ATOM 25630 SG CYS q 88 85.488 90.701 173.460 1.00138.12 S ATOM 25643 SG CYS q 90 88.970 89.820 172.336 1.00147.15 S ATOM 25678 SG CYS q 94 87.167 87.478 174.642 1.00132.97 S ATOM 25700 SG CYS q 97 85.710 87.793 171.224 1.00132.45 S ATOM 33006 SG CYS w 17 75.531 52.481 55.862 1.00161.53 S ATOM 33030 SG CYS w 20 78.954 53.539 57.338 1.00163.91 S ATOM 33191 SG CYS w 39 76.735 56.225 56.482 1.00169.29 S ATOM 33216 SG CYS w 42 78.042 54.009 53.666 1.00167.79 S ATOM 33568 SG CYS w 86 44.242 43.120 86.139 1.00150.39 S ATOM 33592 SG CYS w 89 44.862 39.689 87.859 1.00155.57 S ATOM 33796 SG CYS w 114 46.581 42.853 89.115 1.00146.35 S ATOM 33831 SG CYS w 119 47.377 41.252 85.679 1.00152.45 S ATOM 33941 SG CYS x 7 65.622 72.339 151.593 1.00 98.61 S ATOM 33965 SG CYS x 10 64.034 73.326 154.836 1.00 95.35 S ATOM 34229 SG CYS x 44 61.828 72.499 151.620 1.00107.46 S ATOM 34235 SG CYS x 45 63.278 70.109 154.045 1.00108.23 S ATOM 35381 SG CYS z 19 107.119 61.274 142.359 1.00146.64 S ATOM 35400 SG CYS z 22 107.983 58.701 144.897 1.00145.85 S ATOM 35517 SG CYS z 36 110.703 61.265 143.965 1.00153.01 S ATOM 35543 SG CYS z 39 109.444 58.886 141.303 1.00150.68 S Time building chain proxies: 18.14, per 1000 atoms: 0.51 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 6280 7.00 C 22168 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: 13.65 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 88 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 97 " pdb="ZN ZN q 301 " - pdb=" SG CYS q 90 " pdb=" ZN w 201 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 42 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 20 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 39 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 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: 141 helices and 43 sheets defined 32.5% alpha, 14.9% beta 38 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 17.47 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: 4.169A pdb=" N ALA T 34 " --> pdb=" O GLN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 63 No H-bonds generated for 'chain 'T' and resid 60 through 63' Processing helix chain 'o' and resid 28 through 34 Processing helix chain 'o' and resid 99 through 109 Processing helix chain 'o' and resid 124 through 132 Processing helix chain 'o' and resid 137 through 150 removed outlier: 4.247A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.843A pdb=" N ARG o 227 " --> pdb=" O GLU o 223 " (cutoff:3.500A) Processing helix chain 'o' and resid 230 through 236 Processing helix chain 'o' and resid 245 through 248 No H-bonds generated for 'chain 'o' and resid 245 through 248' Processing helix chain 'o' and resid 275 through 296 Processing helix chain 'o' and resid 302 through 318 Processing helix chain 'o' and resid 339 through 343 Processing helix chain 'o' and resid 349 through 352 No H-bonds generated for 'chain 'o' and resid 349 through 352' Processing helix chain 'o' and resid 382 through 387 Processing helix chain 'o' and resid 399 through 408 Processing helix chain 'o' and resid 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: 4.217A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 539 through 548 Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.838A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.952A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.175A pdb=" N SER o 615 " --> pdb=" O ASP o 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 611 through 615' Processing helix chain 'o' and resid 642 through 645 No H-bonds generated for 'chain 'o' and resid 642 through 645' Processing helix chain 'o' and resid 652 through 660 Processing helix chain 'o' and resid 662 through 683 Processing helix chain 'o' and resid 689 through 692 No H-bonds generated for 'chain 'o' and resid 689 through 692' Processing helix chain 'o' and resid 696 through 721 Processing helix chain 'o' and resid 733 through 759 Processing helix chain 'o' and resid 765 through 772 Processing helix chain 'o' and resid 778 through 785 Processing helix chain 'o' and resid 817 through 820 No H-bonds generated for 'chain 'o' and resid 817 through 820' Processing helix chain 'o' and resid 833 through 867 removed outlier: 4.456A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU o 856 " --> pdb=" O VAL o 852 " (cutoff:3.500A) Processing helix chain 'o' and resid 891 through 893 No H-bonds generated for 'chain 'o' and resid 891 through 893' Processing helix chain 'o' and resid 913 through 920 Processing helix chain 'o' and resid 927 through 933 Processing helix chain 'o' and resid 936 through 944 Processing helix chain 'o' and resid 946 through 969 Processing helix chain 'o' and resid 983 through 993 Processing helix chain 'o' and resid 1006 through 1018 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.104A 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: 3.770A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL o1193 " --> pdb=" O GLN o1190 " (cutoff:3.500A) Processing helix chain 'o' and resid 1218 through 1224 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: 3.819A 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: 3.871A 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: 3.815A pdb=" N THR p 672 " --> pdb=" O LEU p 668 " (cutoff:3.500A) Processing helix chain 'p' and resid 679 through 682 No H-bonds generated for 'chain 'p' and resid 679 through 682' Processing helix chain 'p' and resid 700 through 703 Processing helix chain 'p' and resid 708 through 710 No H-bonds generated for 'chain 'p' and resid 708 through 710' Processing helix chain 'p' and resid 714 through 716 No H-bonds generated for 'chain 'p' and resid 714 through 716' Processing helix chain 'p' and resid 719 through 731 removed outlier: 3.503A pdb=" N THR p 723 " --> pdb=" O SER p 719 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 741 removed outlier: 4.646A 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: 3.551A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.841A 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: 4.085A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.672A 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 24 Processing helix chain 's' and resid 30 through 33 No H-bonds generated for 'chain 's' and resid 30 through 33' Processing helix chain 's' and resid 37 through 44 Processing helix chain 's' and resid 84 through 97 Processing helix chain 's' and resid 112 through 120 Processing helix chain 's' and resid 134 through 136 No H-bonds generated for 'chain 's' and resid 134 through 136' Processing helix chain 's' and resid 139 through 141 No H-bonds generated for 'chain 's' and resid 139 through 141' Processing helix chain 's' and resid 153 through 162 Processing helix chain 's' and resid 178 through 183 Processing helix chain 't' and resid 59 through 75 Processing helix chain 't' and resid 89 through 99 Processing helix chain 'u' and resid 15 through 17 No H-bonds generated for 'chain 'u' and resid 15 through 17' Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'w' and resid 64 through 66 No H-bonds generated for 'chain 'w' and resid 64 through 66' Processing helix chain 'w' and resid 70 through 74 Processing helix chain 'x' and resid 15 through 27 removed outlier: 4.121A pdb=" N TRP x 18 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU x 19 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA x 20 " --> pdb=" O LYS x 17 " (cutoff:3.500A) Processing helix chain 'x' and resid 31 through 38 Processing helix chain 'x' and resid 43 through 50 removed outlier: 3.549A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.681A 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: 3.862A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 112 Processing sheet with id= A, first strand: chain 'S' and resid 27 through 31 removed outlier: 6.825A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 125 through 128 removed outlier: 3.582A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.281A pdb=" N THR T 52 " --> pdb=" O LEU T 85 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU T 85 " --> pdb=" O THR T 52 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL T 54 " --> pdb=" O PHE T 83 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU T 115 " --> pdb=" O LYS T 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'T' and resid 94 through 98 removed outlier: 3.606A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR T 97 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 5.400A 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: 4.626A 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: 3.527A 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: 6.073A 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: 3.957A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.109A 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: 3.580A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.164A 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: 4.343A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.728A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.234A 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: 6.869A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.533A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.454A 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: 6.902A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.448A 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: 6.800A 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: 7.078A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.653A 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: 6.074A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 4.998A 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: 6.290A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 's' and resid 147 through 150 removed outlier: 3.648A pdb=" N GLU s 147 " --> pdb=" O ILE s 194 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 't' and resid 105 through 109 Processing sheet with id= AI, first strand: chain 'u' and resid 2 through 13 removed outlier: 3.554A pdb=" N ALA u 47 " --> pdb=" O ILE u 75 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE u 77 " --> pdb=" O VAL u 45 " (cutoff:3.500A) removed outlier: 5.659A 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: 7.009A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.491A 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: 4.269A pdb=" N SER u 105 " --> pdb=" O ILE u 157 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER u 109 " --> pdb=" O GLY u 161 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.918A 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: 6.837A 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: 5.321A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.728A 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: 6.706A 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 1151 hydrogen bonds defined for protein. 3216 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 19.68 Time building geometry restraints manager: 14.78 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: 8928 1.33 - 1.49: 12581 1.49 - 1.65: 14801 1.65 - 1.81: 325 Bond restraints: 36658 Sorted by residual: bond pdb=" C2' G2L Z 15 " pdb=" C1' G2L Z 15 " 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 15 " pdb=" C3' G2L Z 15 " ideal model delta sigma weight residual 1.270 1.520 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" O3' A Z 14 " pdb=" P G2L Z 15 " ideal model delta sigma weight residual 1.607 1.449 0.158 1.50e-02 4.44e+03 1.11e+02 bond pdb=" N GLY N 5 " pdb=" H GLY N 5 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN N 7 " pdb="HD22 ASN N 7 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 36653 not shown) Histogram of bond angle deviations from ideal: 75.38 - 88.75: 1 88.75 - 102.11: 289 102.11 - 115.47: 24096 115.47 - 128.84: 25330 128.84 - 142.20: 305 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 75.38 34.80 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C07 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " ideal model delta sigma weight residual 110.46 136.31 -25.85 3.00e+00 1.11e-01 7.43e+01 angle pdb=" P26 W0F p1201 " pdb=" O29 W0F p1201 " pdb=" P30 W0F p1201 " ideal model delta sigma weight residual 123.60 142.20 -18.60 3.00e+00 1.11e-01 3.84e+01 angle pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" C10 W0F p1201 " ideal model delta sigma weight residual 99.38 117.50 -18.12 3.00e+00 1.11e-01 3.65e+01 angle pdb=" C ASP s 46 " pdb=" CA ASP s 46 " pdb=" CB ASP s 46 " ideal model delta sigma weight residual 117.23 109.78 7.45 1.36e+00 5.41e-01 3.00e+01 ... (remaining 50016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 20649 23.87 - 47.75: 1161 47.75 - 71.62: 312 71.62 - 95.50: 22 95.50 - 119.37: 4 Dihedral angle restraints: 22148 sinusoidal: 9988 harmonic: 12160 Sorted by residual: dihedral pdb=" O4' C Z 3 " pdb=" C1' C Z 3 " pdb=" N1 C Z 3 " pdb=" C2 C Z 3 " ideal model delta sinusoidal sigma weight residual -160.00 -40.63 -119.37 1 1.50e+01 4.44e-03 6.36e+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 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+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 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 22145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4907 0.074 - 0.149: 639 0.149 - 0.223: 18 0.223 - 0.297: 1 0.297 - 0.371: 3 Chirality restraints: 5568 Sorted by residual: chirality pdb=" C06 W0F p1201 " pdb=" C07 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" O05 W0F p1201 " both_signs ideal model delta sigma weight residual False 2.41 2.04 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA HYP N 8 " pdb=" N HYP N 8 " pdb=" C HYP N 8 " pdb=" CB HYP N 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.10e+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 2.70e+00 ... (remaining 5565 not shown) Planarity restraints: 6103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F p1201 " -0.108 2.00e-02 2.50e+03 4.15e-02 5.16e+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 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C ILE p 51 " 0.078 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.029 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE p 50 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+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: 1.80 - 2.36: 40 2.36 - 2.92: 14914 2.92 - 3.48: 40884 3.48 - 4.04: 71324 4.04 - 4.60: 103083 Nonbonded interactions: 230245 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.799 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 1.948 2.050 nonbonded pdb="HG22 ILE N 4 " pdb="HD13 ILE N 4 " model vdw 2.021 2.440 nonbonded pdb=" OD2 ASP o 497 " pdb=" O33 W0F p1201 " model vdw 2.046 2.800 ... (remaining 230240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.940 Extract box with map and model: 8.740 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 113.340 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.251 36635 Z= 0.546 Angle : 0.777 34.798 49969 Z= 0.399 Chirality : 0.048 0.371 5568 Planarity : 0.005 0.067 6099 Dihedral : 15.372 119.373 14275 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.89 % Favored : 95.91 % Rotamer: Outliers : 1.17 % Allowed : 5.91 % Favored : 92.92 % 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: 0.47 (0.13), residues: 4137 helix: 1.24 (0.14), residues: 1415 sheet: 0.22 (0.19), residues: 666 loop : -0.23 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP o1192 HIS 0.007 0.001 HIS o 809 PHE 0.022 0.002 PHE o 548 TYR 0.035 0.002 TYR o 669 ARG 0.005 0.001 ARG o 546 *********************** 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 1049 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1006 time to evaluate : 4.251 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: o 18 ILE cc_start: 0.8048 (mt) cc_final: 0.7763 (mp) REVERT: o 19 LYS cc_start: 0.7551 (mttp) cc_final: 0.7335 (mmtt) REVERT: o 34 MET cc_start: 0.7085 (ttp) cc_final: 0.6644 (ptm) REVERT: o 138 LYS cc_start: 0.7504 (tttm) cc_final: 0.7302 (ttpt) REVERT: o 139 LYS cc_start: 0.6922 (ttmt) cc_final: 0.6683 (mptt) REVERT: o 151 LYS cc_start: 0.7356 (mmtp) cc_final: 0.7135 (mtpp) REVERT: o 193 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7882 (tmm-80) REVERT: o 234 PHE cc_start: 0.7442 (t80) cc_final: 0.7188 (t80) REVERT: o 306 ASP cc_start: 0.8040 (m-30) cc_final: 0.7826 (m-30) REVERT: o 346 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7474 (ptpp) REVERT: o 347 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7338 (mp0) REVERT: o 397 PHE cc_start: 0.7466 (p90) cc_final: 0.7108 (p90) REVERT: o 495 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.5863 (p0) REVERT: o 499 ASP cc_start: 0.7302 (m-30) cc_final: 0.6829 (m-30) REVERT: o 508 SER cc_start: 0.6755 (t) cc_final: 0.6207 (p) REVERT: o 524 MET cc_start: 0.7764 (mmp) cc_final: 0.7360 (mmm) REVERT: o 565 MET cc_start: 0.8268 (tpt) cc_final: 0.8038 (mmt) REVERT: o 573 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7208 (mtmm) REVERT: o 600 ILE cc_start: 0.8002 (mt) cc_final: 0.7783 (mm) REVERT: o 621 ILE cc_start: 0.6423 (mm) cc_final: 0.6022 (mm) REVERT: o 794 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8321 (mt-10) REVERT: o 841 MET cc_start: 0.7380 (mtp) cc_final: 0.7158 (mtm) REVERT: o 868 MET cc_start: 0.7078 (ptt) cc_final: 0.6724 (ptm) REVERT: o 872 MET cc_start: 0.7861 (ttp) cc_final: 0.7523 (ttm) REVERT: o 876 ASP cc_start: 0.7783 (m-30) cc_final: 0.7548 (t0) REVERT: o 919 LYS cc_start: 0.6931 (mttt) cc_final: 0.6679 (mtmt) REVERT: o 1063 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7112 (mp0) REVERT: o 1132 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8235 (mppt) REVERT: o 1219 LYS cc_start: 0.9161 (mttt) cc_final: 0.8899 (tppp) REVERT: o 1259 ILE cc_start: 0.8175 (mt) cc_final: 0.7626 (mm) REVERT: o 1282 ASP cc_start: 0.8365 (p0) cc_final: 0.8057 (p0) REVERT: o 1295 ASP cc_start: 0.8317 (m-30) cc_final: 0.8058 (m-30) REVERT: o 1305 SER cc_start: 0.7746 (t) cc_final: 0.7444 (p) REVERT: o 1306 LYS cc_start: 0.6949 (mttt) cc_final: 0.6372 (mmmm) REVERT: o 1339 ASP cc_start: 0.6906 (t0) cc_final: 0.6327 (m-30) REVERT: o 1383 TYR cc_start: 0.7321 (t80) cc_final: 0.7022 (t80) REVERT: o 1389 ASP cc_start: 0.8482 (m-30) cc_final: 0.8088 (p0) REVERT: o 1391 SER cc_start: 0.7768 (t) cc_final: 0.6851 (p) REVERT: o 1398 LEU cc_start: 0.7251 (mt) cc_final: 0.6780 (tp) REVERT: o 1422 GLN cc_start: 0.5721 (mt0) cc_final: 0.5356 (mp10) REVERT: o 1423 ASP cc_start: 0.7475 (m-30) cc_final: 0.7108 (t0) REVERT: p 89 GLU cc_start: 0.7347 (tt0) cc_final: 0.6899 (tm-30) REVERT: p 109 MET cc_start: 0.7323 (mmm) cc_final: 0.7009 (mmm) REVERT: p 200 MET cc_start: 0.7507 (ttm) cc_final: 0.7301 (ttp) REVERT: p 233 SER cc_start: 0.6861 (t) cc_final: 0.6273 (p) REVERT: p 291 ASP cc_start: 0.7520 (t0) cc_final: 0.7319 (t0) REVERT: p 307 GLU cc_start: 0.8667 (tp30) cc_final: 0.8333 (tt0) REVERT: p 335 ARG cc_start: 0.6813 (mtm180) cc_final: 0.6421 (mtp180) REVERT: p 345 LYS cc_start: 0.7248 (mptt) cc_final: 0.7008 (mmtm) REVERT: p 367 TYR cc_start: 0.6651 (t80) cc_final: 0.6277 (t80) REVERT: p 381 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7870 (pm20) REVERT: p 386 ASP cc_start: 0.6725 (m-30) cc_final: 0.6096 (m-30) REVERT: p 438 ARG cc_start: 0.6159 (mtt180) cc_final: 0.5897 (mmp80) REVERT: p 442 ASP cc_start: 0.6120 (m-30) cc_final: 0.5658 (m-30) REVERT: p 471 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7140 (t0) REVERT: p 477 SER cc_start: 0.7620 (t) cc_final: 0.7278 (p) REVERT: p 542 LEU cc_start: 0.6556 (mt) cc_final: 0.6290 (mt) REVERT: p 543 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6796 (mt-10) REVERT: p 551 GLU cc_start: 0.7508 (mp0) cc_final: 0.6640 (pm20) REVERT: p 601 VAL cc_start: 0.8146 (t) cc_final: 0.7847 (t) REVERT: p 606 ASP cc_start: 0.5960 (t0) cc_final: 0.5574 (p0) REVERT: p 610 ARG cc_start: 0.5554 (mtt90) cc_final: 0.4810 (mtm-85) REVERT: p 671 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6421 (mt-10) REVERT: p 677 MET cc_start: 0.7933 (mmm) cc_final: 0.6046 (mmt) REVERT: p 697 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7569 (mt-10) REVERT: p 733 MET cc_start: 0.8477 (mtt) cc_final: 0.8135 (ttm) REVERT: p 745 ASP cc_start: 0.7018 (m-30) cc_final: 0.6635 (m-30) REVERT: p 796 MET cc_start: 0.8386 (mtm) cc_final: 0.7935 (mtm) REVERT: p 828 VAL cc_start: 0.7151 (t) cc_final: 0.6861 (p) REVERT: p 870 THR cc_start: 0.8364 (p) cc_final: 0.7712 (p) REVERT: p 905 ASP cc_start: 0.7649 (t0) cc_final: 0.6996 (t0) REVERT: p 1054 MET cc_start: 0.8471 (mtm) cc_final: 0.7982 (mtm) REVERT: p 1064 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: p 1080 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7366 (mtp85) REVERT: p 1101 GLN cc_start: 0.7891 (tt0) cc_final: 0.7681 (tt0) REVERT: p 1121 LEU cc_start: 0.8317 (mt) cc_final: 0.8101 (mp) REVERT: p 1124 ILE cc_start: 0.7705 (mt) cc_final: 0.7497 (pp) REVERT: p 1125 MET cc_start: 0.7609 (mtm) cc_final: 0.7341 (mtt) REVERT: p 1151 MET cc_start: 0.8014 (ptm) cc_final: 0.7804 (ptm) REVERT: p 1163 MET cc_start: 0.6891 (mtp) cc_final: 0.6590 (mtm) REVERT: q 41 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6657 (tm-30) REVERT: q 51 GLN cc_start: 0.7799 (tt0) cc_final: 0.6853 (pt0) REVERT: q 108 ASN cc_start: 0.6277 (m-40) cc_final: 0.6044 (p0) REVERT: q 121 ILE cc_start: 0.8275 (mt) cc_final: 0.8020 (mp) REVERT: q 126 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6825 (mmm-85) REVERT: q 155 LYS cc_start: 0.6743 (tttt) cc_final: 0.6527 (tttm) REVERT: q 242 GLU cc_start: 0.7877 (pt0) cc_final: 0.7603 (pm20) REVERT: r 62 MET cc_start: 0.8891 (mmt) cc_final: 0.8664 (mmt) REVERT: s 70 ASP cc_start: 0.8425 (m-30) cc_final: 0.8204 (t0) REVERT: s 91 CYS cc_start: 0.8734 (t) cc_final: 0.8351 (t) REVERT: s 177 ASP cc_start: 0.8067 (t70) cc_final: 0.7728 (t70) REVERT: s 210 GLN cc_start: 0.6644 (mt0) cc_final: 0.5665 (tm-30) REVERT: t 52 ILE cc_start: 0.8822 (pt) cc_final: 0.8555 (pt) REVERT: t 79 VAL cc_start: 0.7665 (t) cc_final: 0.7297 (m) REVERT: t 80 MET cc_start: 0.8109 (mmt) cc_final: 0.7381 (mpt) REVERT: t 86 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7598 (mm-30) REVERT: t 87 THR cc_start: 0.8478 (p) cc_final: 0.8255 (p) REVERT: u 73 LYS cc_start: 0.7373 (mmtt) cc_final: 0.7170 (mmmt) REVERT: u 86 ASP cc_start: -0.0472 (m-30) cc_final: -0.0690 (m-30) REVERT: u 104 MET cc_start: 0.8722 (ttp) cc_final: 0.8422 (ppp) REVERT: u 165 ASP cc_start: 0.8051 (m-30) cc_final: 0.7709 (t0) REVERT: v 18 GLU cc_start: 0.7780 (mp0) cc_final: 0.7436 (mp0) REVERT: v 23 ASP cc_start: 0.7781 (m-30) cc_final: 0.7331 (m-30) REVERT: v 31 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6490 (mp0) REVERT: v 51 ASP cc_start: 0.7509 (m-30) cc_final: 0.7165 (p0) REVERT: v 63 THR cc_start: 0.9021 (p) cc_final: 0.8646 (t) REVERT: v 76 ASN cc_start: 0.8410 (m-40) cc_final: 0.7857 (m-40) REVERT: v 100 GLU cc_start: 0.6764 (tt0) cc_final: 0.6262 (tp30) REVERT: v 126 GLN cc_start: 0.7263 (tt0) cc_final: 0.6992 (tt0) REVERT: w 44 TYR cc_start: 0.7868 (t80) cc_final: 0.7245 (t80) REVERT: w 71 ASP cc_start: 0.8173 (m-30) cc_final: 0.7922 (m-30) REVERT: x 62 TYR cc_start: 0.7646 (m-80) cc_final: 0.6755 (m-80) REVERT: y 38 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7484 (mm-30) REVERT: y 48 SER cc_start: 0.7901 (t) cc_final: 0.7690 (p) REVERT: y 70 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7894 (ttmm) REVERT: z 46 LYS cc_start: 0.7295 (tptp) cc_final: 0.6845 (tptt) outliers start: 43 outliers final: 13 residues processed: 1033 average time/residue: 1.6680 time to fit residues: 2029.5381 Evaluate side-chains 645 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 630 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 675 VAL Chi-restraints excluded: chain o residue 728 THR 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 235 ILE Chi-restraints excluded: chain p residue 402 PHE Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 594 MET Chi-restraints excluded: chain p residue 598 VAL Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 0.9990 chunk 319 optimal weight: 0.1980 chunk 177 optimal weight: 0.0870 chunk 109 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 329 optimal weight: 40.0000 chunk 127 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 245 optimal weight: 0.5980 chunk 382 optimal weight: 0.0570 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 178 GLN o 62 GLN o 181 HIS ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN o 531 ASN ** o 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 700 GLN o 721 HIS o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN o 935 GLN ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1462 GLN p 43 GLN p 111 ASN p 164 ASN p 245 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 481 HIS ** p 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 525 ASN p 631 GLN p 639 HIS p 649 ASN p 699 HIS ** p 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 838 GLN ** p 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 941 GLN p 948 GLN p1007 ASN p1021 HIS p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN r 66 ASN r 129 GLN ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 44 ASN v 130 ASN w 22 ASN w 41 ASN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 113 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 36635 Z= 0.142 Angle : 0.471 9.706 49969 Z= 0.253 Chirality : 0.040 0.205 5568 Planarity : 0.003 0.060 6099 Dihedral : 17.013 140.408 5847 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 26.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 3.28 % Allowed : 16.43 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.13), residues: 4137 helix: 1.92 (0.14), residues: 1403 sheet: 0.27 (0.19), residues: 688 loop : -0.08 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP o1192 HIS 0.008 0.001 HIS p 842 PHE 0.015 0.001 PHE o 431 TYR 0.019 0.001 TYR o1197 ARG 0.005 0.000 ARG o 426 *********************** 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 787 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 666 time to evaluate : 4.314 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: o 16 ARG cc_start: 0.7102 (mmt90) cc_final: 0.6784 (mmt90) REVERT: o 20 ARG cc_start: 0.6601 (ttp80) cc_final: 0.6326 (ttp-110) REVERT: o 34 MET cc_start: 0.7004 (ttp) cc_final: 0.6798 (ptm) REVERT: o 38 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7396 (mt-10) REVERT: o 61 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6644 (ptm160) REVERT: o 112 PHE cc_start: 0.7727 (t80) cc_final: 0.7438 (t80) REVERT: o 192 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7242 (ttp-110) REVERT: o 347 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7322 (mp0) REVERT: o 387 ASN cc_start: 0.7310 (m-40) cc_final: 0.7014 (t0) REVERT: o 397 PHE cc_start: 0.7310 (p90) cc_final: 0.7008 (p90) REVERT: o 425 ASP cc_start: 0.6603 (m-30) cc_final: 0.6120 (p0) REVERT: o 495 ASP cc_start: 0.6220 (OUTLIER) cc_final: 0.5881 (p0) REVERT: o 508 SER cc_start: 0.6451 (t) cc_final: 0.5823 (p) REVERT: o 565 MET cc_start: 0.8370 (tpt) cc_final: 0.8063 (mmt) REVERT: o 683 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: o 725 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7994 (tt) REVERT: o 743 ARG cc_start: 0.6888 (ttp80) cc_final: 0.6637 (ttm-80) REVERT: o 762 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7568 (pt0) REVERT: o 868 MET cc_start: 0.7304 (ptt) cc_final: 0.6919 (ptm) REVERT: o 919 LYS cc_start: 0.6792 (mttt) cc_final: 0.6589 (mmmt) REVERT: o 945 ASN cc_start: 0.6861 (t0) cc_final: 0.6556 (t0) REVERT: o 957 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7419 (mm-30) REVERT: o 976 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7135 (tptt) REVERT: o 1063 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6979 (mp0) REVERT: o 1132 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8399 (mppt) REVERT: o 1218 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8300 (mmm-85) REVERT: o 1259 ILE cc_start: 0.8128 (mt) cc_final: 0.7770 (mm) REVERT: o 1284 PHE cc_start: 0.7729 (t80) cc_final: 0.7138 (t80) REVERT: o 1306 LYS cc_start: 0.6751 (mttt) cc_final: 0.6152 (mmmt) REVERT: o 1339 ASP cc_start: 0.6878 (t0) cc_final: 0.6401 (m-30) REVERT: o 1383 TYR cc_start: 0.7338 (t80) cc_final: 0.7090 (t80) REVERT: o 1389 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8119 (p0) REVERT: o 1391 SER cc_start: 0.7812 (t) cc_final: 0.7057 (p) REVERT: o 1398 LEU cc_start: 0.7119 (mt) cc_final: 0.6655 (tp) REVERT: o 1422 GLN cc_start: 0.5690 (mt0) cc_final: 0.5478 (mp10) REVERT: o 1423 ASP cc_start: 0.7292 (m-30) cc_final: 0.7091 (t0) REVERT: p 36 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: p 89 GLU cc_start: 0.7025 (tt0) cc_final: 0.6778 (tm-30) REVERT: p 109 MET cc_start: 0.7552 (mmm) cc_final: 0.7106 (mmm) REVERT: p 233 SER cc_start: 0.6585 (t) cc_final: 0.6303 (p) REVERT: p 266 GLU cc_start: 0.7688 (pp20) cc_final: 0.7450 (pp20) REVERT: p 291 ASP cc_start: 0.7669 (t0) cc_final: 0.7430 (t0) REVERT: p 335 ARG cc_start: 0.6723 (mtm180) cc_final: 0.6355 (mtp180) REVERT: p 345 LYS cc_start: 0.7311 (mptt) cc_final: 0.7064 (mmtm) REVERT: p 379 ARG cc_start: 0.7479 (mtt180) cc_final: 0.7278 (mtt90) REVERT: p 381 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7856 (pm20) REVERT: p 386 ASP cc_start: 0.6832 (m-30) cc_final: 0.6274 (m-30) REVERT: p 414 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5203 (mp0) REVERT: p 438 ARG cc_start: 0.6211 (mtt180) cc_final: 0.5983 (mmp80) REVERT: p 442 ASP cc_start: 0.5973 (m-30) cc_final: 0.5564 (m-30) REVERT: p 543 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6756 (mt-10) REVERT: p 606 ASP cc_start: 0.5948 (t0) cc_final: 0.5195 (p0) REVERT: p 697 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7610 (mt-10) REVERT: p 745 ASP cc_start: 0.6977 (m-30) cc_final: 0.6631 (m-30) REVERT: p 796 MET cc_start: 0.8456 (mtm) cc_final: 0.8198 (ttm) REVERT: p 816 GLU cc_start: 0.8851 (tp30) cc_final: 0.8629 (tp30) REVERT: p 828 VAL cc_start: 0.7236 (t) cc_final: 0.6859 (p) REVERT: p 905 ASP cc_start: 0.7768 (t0) cc_final: 0.7121 (t0) REVERT: p 952 GLU cc_start: 0.7197 (pt0) cc_final: 0.6795 (pm20) REVERT: p 1054 MET cc_start: 0.8434 (mtm) cc_final: 0.8177 (mtm) REVERT: p 1080 ARG cc_start: 0.7909 (mtt90) cc_final: 0.7376 (mtp85) REVERT: p 1121 LEU cc_start: 0.8266 (mt) cc_final: 0.7916 (mt) REVERT: p 1163 MET cc_start: 0.6827 (mtp) cc_final: 0.6587 (mtm) REVERT: q 17 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7478 (tt0) REVERT: q 41 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6675 (tm-30) REVERT: q 51 GLN cc_start: 0.7907 (tt0) cc_final: 0.6806 (pt0) REVERT: q 83 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7422 (mt0) REVERT: q 126 ARG cc_start: 0.7233 (mtt180) cc_final: 0.6937 (mmm-85) REVERT: q 185 GLU cc_start: 0.8003 (tt0) cc_final: 0.7688 (mt-10) REVERT: q 234 GLU cc_start: 0.7509 (tt0) cc_final: 0.6230 (tm-30) REVERT: r 62 MET cc_start: 0.8893 (mmt) cc_final: 0.8233 (mmm) REVERT: s 177 ASP cc_start: 0.8056 (t70) cc_final: 0.7606 (t70) REVERT: s 210 GLN cc_start: 0.6496 (mt0) cc_final: 0.6066 (tm-30) REVERT: t 82 GLU cc_start: 0.8224 (pm20) cc_final: 0.7882 (pm20) REVERT: t 86 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7547 (mt-10) REVERT: t 87 THR cc_start: 0.8527 (p) cc_final: 0.8326 (p) REVERT: u 1 MET cc_start: 0.8113 (tpp) cc_final: 0.7112 (pp-130) REVERT: v 18 GLU cc_start: 0.7905 (mp0) cc_final: 0.7533 (mp0) REVERT: v 23 ASP cc_start: 0.7700 (m-30) cc_final: 0.6795 (m-30) REVERT: v 36 LYS cc_start: 0.6212 (mmpt) cc_final: 0.5793 (mmpt) REVERT: v 76 ASN cc_start: 0.8168 (m-40) cc_final: 0.7684 (m-40) REVERT: v 100 GLU cc_start: 0.6708 (tt0) cc_final: 0.6338 (tp30) REVERT: w 15 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7472 (pmm-80) REVERT: w 44 TYR cc_start: 0.7576 (t80) cc_final: 0.7333 (t80) REVERT: w 71 ASP cc_start: 0.8241 (m-30) cc_final: 0.7944 (m-30) REVERT: x 62 TYR cc_start: 0.7777 (m-80) cc_final: 0.6560 (m-80) REVERT: y 48 SER cc_start: 0.7944 (t) cc_final: 0.7692 (p) REVERT: y 70 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7892 (ttmm) REVERT: z 15 MET cc_start: 0.6105 (mpm) cc_final: 0.5724 (mmt) REVERT: z 56 ASP cc_start: 0.6780 (m-30) cc_final: 0.6125 (p0) outliers start: 121 outliers final: 51 residues processed: 740 average time/residue: 1.5088 time to fit residues: 1335.1075 Evaluate side-chains 637 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 578 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 117 LEU Chi-restraints excluded: chain o residue 221 VAL Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 515 ILE Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 725 LEU Chi-restraints excluded: chain o residue 940 LYS Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1139 LEU Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1233 GLU Chi-restraints excluded: chain o residue 1245 CYS Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 541 ILE Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 572 CYS Chi-restraints excluded: chain p residue 629 GLU Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 815 LYS Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 236 CYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain s residue 13 ILE Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain u residue 3 TYR Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 120 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 55 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain z residue 53 VAL 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: 0.0770 chunk 260 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 383 optimal weight: 0.1980 chunk 413 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 379 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 overall best weight: 1.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN o 136 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 539 GLN o 765 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 947 HIS ** o1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1032 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1220 HIS p 265 GLN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 471 ASN p 481 HIS p 500 GLN ** p 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 980 HIS ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 46 GLN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 44 ASN v 126 GLN v 130 ASN w 22 ASN w 41 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: 0.5616 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 36635 Z= 0.385 Angle : 0.597 15.113 49969 Z= 0.314 Chirality : 0.044 0.185 5568 Planarity : 0.005 0.071 6099 Dihedral : 16.806 146.281 5827 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 28.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.35 % Favored : 95.46 % Rotamer: Outliers : 5.42 % Allowed : 16.57 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4137 helix: 1.54 (0.14), residues: 1414 sheet: 0.16 (0.19), residues: 673 loop : -0.23 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP o 479 HIS 0.018 0.002 HIS r 43 PHE 0.025 0.002 PHE q 63 TYR 0.019 0.002 TYR p1048 ARG 0.010 0.001 ARG o 475 *********************** 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 789 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 589 time to evaluate : 4.080 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: o 16 ARG cc_start: 0.7244 (mmt90) cc_final: 0.6903 (mmt90) REVERT: o 38 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7680 (mt-10) REVERT: o 61 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6621 (ptm160) REVERT: o 112 PHE cc_start: 0.7821 (t80) cc_final: 0.7471 (t80) REVERT: o 151 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6694 (mtpp) REVERT: o 192 ARG cc_start: 0.7815 (mtp-110) cc_final: 0.7246 (ttp-110) REVERT: o 305 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7082 (tm-30) REVERT: o 325 LEU cc_start: 0.8735 (tp) cc_final: 0.8502 (mp) REVERT: o 329 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7591 (ttp) REVERT: o 425 ASP cc_start: 0.6632 (m-30) cc_final: 0.5927 (p0) REVERT: o 426 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.6927 (mtm-85) REVERT: o 561 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7131 (mtm) REVERT: o 683 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: o 712 ASP cc_start: 0.6687 (m-30) cc_final: 0.6432 (m-30) REVERT: o 725 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7965 (tt) REVERT: o 868 MET cc_start: 0.7188 (ptt) cc_final: 0.6972 (ptt) REVERT: o 876 ASP cc_start: 0.7382 (t0) cc_final: 0.6917 (t0) REVERT: o 902 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7115 (pt0) REVERT: o 945 ASN cc_start: 0.7343 (t0) cc_final: 0.7038 (t0) REVERT: o 976 LYS cc_start: 0.7578 (ttmt) cc_final: 0.6881 (tptt) REVERT: o 1063 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7230 (mp0) REVERT: o 1132 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8365 (mppt) REVERT: o 1144 LEU cc_start: 0.7754 (tp) cc_final: 0.7521 (tp) REVERT: o 1168 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7826 (mttp) REVERT: o 1259 ILE cc_start: 0.8049 (mt) cc_final: 0.7718 (mm) REVERT: o 1306 LYS cc_start: 0.6854 (mttt) cc_final: 0.6307 (mmmt) REVERT: o 1339 ASP cc_start: 0.6734 (t0) cc_final: 0.6455 (m-30) REVERT: o 1383 TYR cc_start: 0.7373 (t80) cc_final: 0.7123 (t80) REVERT: o 1391 SER cc_start: 0.8184 (t) cc_final: 0.7364 (p) REVERT: o 1423 ASP cc_start: 0.7653 (m-30) cc_final: 0.7175 (t0) REVERT: p 17 ILE cc_start: 0.8918 (mt) cc_final: 0.8660 (mm) REVERT: p 89 GLU cc_start: 0.7069 (tt0) cc_final: 0.6838 (tm-30) REVERT: p 90 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.6092 (tt0) REVERT: p 109 MET cc_start: 0.6900 (mmm) cc_final: 0.6548 (mmm) REVERT: p 152 ILE cc_start: 0.7631 (mt) cc_final: 0.7408 (mm) REVERT: p 168 ASP cc_start: 0.6908 (p0) cc_final: 0.6572 (m-30) REVERT: p 233 SER cc_start: 0.6942 (t) cc_final: 0.6633 (p) REVERT: p 297 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7341 (mmm) REVERT: p 335 ARG cc_start: 0.6725 (mtm180) cc_final: 0.6322 (mtp180) REVERT: p 381 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7710 (mp0) REVERT: p 386 ASP cc_start: 0.6810 (m-30) cc_final: 0.6425 (m-30) REVERT: p 388 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6589 (m-80) REVERT: p 414 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5249 (mp0) REVERT: p 442 ASP cc_start: 0.6492 (m-30) cc_final: 0.6172 (m-30) REVERT: p 471 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7017 (t0) REVERT: p 543 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7404 (mt-10) REVERT: p 588 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6250 (mtt90) REVERT: p 597 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7479 (mp) REVERT: p 598 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7477 (m) REVERT: p 600 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7117 (pt0) REVERT: p 601 VAL cc_start: 0.8635 (t) cc_final: 0.8210 (p) REVERT: p 630 LYS cc_start: 0.6847 (mttt) cc_final: 0.6438 (mmtm) REVERT: p 745 ASP cc_start: 0.7734 (m-30) cc_final: 0.7504 (m-30) REVERT: p 747 LEU cc_start: 0.8168 (mt) cc_final: 0.7759 (mp) REVERT: p 796 MET cc_start: 0.8538 (mtm) cc_final: 0.8305 (ttm) REVERT: p 952 GLU cc_start: 0.7361 (pt0) cc_final: 0.6962 (pm20) REVERT: p 958 CYS cc_start: 0.8081 (p) cc_final: 0.7827 (p) REVERT: p 1080 ARG cc_start: 0.7831 (mtt90) cc_final: 0.7202 (mtp85) REVERT: p 1106 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6721 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8254 (mt) cc_final: 0.7911 (mt) REVERT: p 1131 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.8312 (mtp85) REVERT: p 1138 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.5590 (mmt90) REVERT: p 1163 MET cc_start: 0.6940 (mtp) cc_final: 0.6649 (mtm) REVERT: q 6 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: q 17 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7448 (tt0) REVERT: q 41 GLU cc_start: 0.7849 (mt-10) cc_final: 0.6604 (tm-30) REVERT: q 83 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: q 111 GLN cc_start: 0.7947 (tt0) cc_final: 0.7529 (mp10) REVERT: q 126 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6939 (mmm-85) REVERT: q 160 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.5859 (mtm-85) REVERT: q 185 GLU cc_start: 0.8171 (tt0) cc_final: 0.7669 (tt0) REVERT: q 234 GLU cc_start: 0.7572 (tt0) cc_final: 0.6980 (tt0) REVERT: q 259 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7355 (tp) REVERT: s 99 ILE cc_start: 0.7930 (mt) cc_final: 0.7618 (mm) REVERT: s 117 SER cc_start: 0.8069 (t) cc_final: 0.7865 (p) REVERT: s 187 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7320 (ttm110) REVERT: s 210 GLN cc_start: 0.6410 (mt0) cc_final: 0.5866 (tm-30) REVERT: t 82 GLU cc_start: 0.8473 (pm20) cc_final: 0.8179 (pm20) REVERT: t 86 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7593 (mt-10) REVERT: t 101 LYS cc_start: 0.6769 (OUTLIER) cc_final: 0.5700 (mptp) REVERT: u 117 MET cc_start: 0.1637 (mmp) cc_final: 0.1037 (mtt) REVERT: v 18 GLU cc_start: 0.8184 (mp0) cc_final: 0.7847 (mp0) REVERT: v 23 ASP cc_start: 0.7635 (m-30) cc_final: 0.7276 (m-30) REVERT: v 95 LYS cc_start: 0.6825 (tttt) cc_final: 0.6478 (ttmt) REVERT: v 100 GLU cc_start: 0.6945 (tt0) cc_final: 0.6403 (mm-30) REVERT: v 141 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7350 (p) REVERT: w 15 ARG cc_start: 0.7919 (ptp90) cc_final: 0.7540 (pmm-80) REVERT: w 21 ASN cc_start: 0.7665 (m-40) cc_final: 0.7383 (m-40) REVERT: w 44 TYR cc_start: 0.7732 (t80) cc_final: 0.7502 (t80) REVERT: w 71 ASP cc_start: 0.8312 (m-30) cc_final: 0.8099 (m-30) REVERT: w 74 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: w 82 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: x 62 TYR cc_start: 0.8122 (m-80) cc_final: 0.7922 (m-80) REVERT: y 23 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7303 (tttm) REVERT: y 48 SER cc_start: 0.8046 (t) cc_final: 0.7760 (p) REVERT: y 70 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8162 (ttmm) REVERT: z 15 MET cc_start: 0.6315 (mpm) cc_final: 0.5848 (mmt) REVERT: z 46 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7351 (tptt) REVERT: z 56 ASP cc_start: 0.6995 (m-30) cc_final: 0.6510 (p0) outliers start: 200 outliers final: 107 residues processed: 717 average time/residue: 1.5199 time to fit residues: 1304.7451 Evaluate side-chains 680 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 545 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 151 LYS Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 251 THR Chi-restraints excluded: chain o residue 253 LEU Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 561 MET Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 683 GLU Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 725 LEU Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 803 LYS Chi-restraints excluded: chain o residue 847 LEU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 902 GLU Chi-restraints excluded: chain o residue 977 VAL Chi-restraints excluded: chain o residue 1021 VAL Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1221 MET Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1245 CYS Chi-restraints excluded: chain o residue 1309 MET Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1332 GLN Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1341 VAL Chi-restraints excluded: chain o residue 1367 THR Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 53 MET Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 126 VAL Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 193 VAL Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 240 LEU Chi-restraints excluded: chain p residue 294 ASP Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 348 LEU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 522 LEU Chi-restraints excluded: chain p residue 588 ARG Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 598 VAL Chi-restraints excluded: chain p residue 638 ARG Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 784 SER Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 851 ASP Chi-restraints excluded: chain p residue 870 THR Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1138 ARG Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 106 ARG Chi-restraints excluded: chain q residue 160 ARG Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain q residue 259 LEU Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 101 LYS Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain u residue 120 ASP Chi-restraints excluded: chain v residue 25 VAL Chi-restraints excluded: chain v residue 31 GLU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain v residue 146 LYS Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 74 GLN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain y residue 19 ILE Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain y residue 110 LYS Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain z residue 52 LEU 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: 2.9990 chunk 287 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 257 optimal weight: 0.5980 chunk 384 optimal weight: 0.8980 chunk 406 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 62 GLN o 136 GLN o 204 HIS ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 926 ASN o 947 HIS o1163 HIS o1360 ASN ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 471 ASN ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 948 GLN ** p1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 107 GLN ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN v 130 ASN w 46 GLN w 50 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36635 Z= 0.239 Angle : 0.478 9.800 49969 Z= 0.255 Chirality : 0.040 0.172 5568 Planarity : 0.003 0.057 6099 Dihedral : 16.528 113.595 5822 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 29.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.60 % Rotamer: Outliers : 4.80 % Allowed : 19.12 % Favored : 76.08 % 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: 0.78 (0.13), residues: 4137 helix: 1.80 (0.14), residues: 1411 sheet: 0.10 (0.19), residues: 691 loop : -0.19 (0.14), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP o1192 HIS 0.015 0.001 HIS r 43 PHE 0.012 0.001 PHE p 364 TYR 0.015 0.001 TYR r 67 ARG 0.006 0.000 ARG u 63 *********************** 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 741 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 564 time to evaluate : 3.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.7237 (mmt90) cc_final: 0.6877 (mmt90) REVERT: o 38 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7699 (mt-10) REVERT: o 45 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: o 61 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6553 (ptm160) REVERT: o 112 PHE cc_start: 0.7649 (t80) cc_final: 0.7347 (t80) REVERT: o 192 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7076 (ttp-110) REVERT: o 201 GLU cc_start: 0.7430 (tt0) cc_final: 0.7084 (pt0) REVERT: o 305 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7120 (tm-30) REVERT: o 329 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.6932 (ttp) REVERT: o 425 ASP cc_start: 0.6631 (m-30) cc_final: 0.5911 (p0) REVERT: o 426 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.6941 (mtm-85) REVERT: o 683 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: o 712 ASP cc_start: 0.6588 (m-30) cc_final: 0.6324 (m-30) REVERT: o 725 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8077 (tt) REVERT: o 818 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7188 (pm20) REVERT: o 868 MET cc_start: 0.7181 (ptt) cc_final: 0.6914 (ptt) REVERT: o 872 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7529 (ttm) REVERT: o 876 ASP cc_start: 0.7683 (t0) cc_final: 0.7173 (t0) REVERT: o 902 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7162 (pt0) REVERT: o 945 ASN cc_start: 0.7201 (t0) cc_final: 0.6934 (t0) REVERT: o 959 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7559 (mtp) REVERT: o 976 LYS cc_start: 0.7644 (ttmt) cc_final: 0.6992 (tptt) REVERT: o 1063 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7131 (mp0) REVERT: o 1132 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8380 (mppt) REVERT: o 1168 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7827 (mttp) REVERT: o 1259 ILE cc_start: 0.8010 (mt) cc_final: 0.7799 (mp) REVERT: o 1306 LYS cc_start: 0.6867 (mttt) cc_final: 0.6264 (mmmt) REVERT: o 1332 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: o 1339 ASP cc_start: 0.6705 (t0) cc_final: 0.6489 (m-30) REVERT: o 1383 TYR cc_start: 0.7366 (t80) cc_final: 0.7120 (t80) REVERT: o 1391 SER cc_start: 0.8015 (t) cc_final: 0.7461 (p) REVERT: o 1423 ASP cc_start: 0.7726 (m-30) cc_final: 0.6994 (t0) REVERT: p 17 ILE cc_start: 0.8985 (mt) cc_final: 0.8658 (mm) REVERT: p 36 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: p 89 GLU cc_start: 0.7299 (tt0) cc_final: 0.7073 (tm-30) REVERT: p 90 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.5982 (tt0) REVERT: p 109 MET cc_start: 0.6985 (mmm) cc_final: 0.6599 (mmm) REVERT: p 152 ILE cc_start: 0.7900 (mt) cc_final: 0.7669 (mm) REVERT: p 168 ASP cc_start: 0.6908 (p0) cc_final: 0.6611 (m-30) REVERT: p 193 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7549 (p) REVERT: p 233 SER cc_start: 0.6685 (t) cc_final: 0.6429 (p) REVERT: p 265 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: p 290 TYR cc_start: 0.7633 (m-80) cc_final: 0.7304 (m-80) REVERT: p 297 MET cc_start: 0.7647 (mtm) cc_final: 0.7302 (mmm) REVERT: p 335 ARG cc_start: 0.6724 (mtm180) cc_final: 0.6387 (mtm-85) REVERT: p 381 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7718 (mp0) REVERT: p 386 ASP cc_start: 0.6568 (m-30) cc_final: 0.6220 (m-30) REVERT: p 388 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7284 (m-80) REVERT: p 414 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5178 (mp0) REVERT: p 597 ILE cc_start: 0.8229 (mm) cc_final: 0.7902 (mp) REVERT: p 598 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7402 (m) REVERT: p 600 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6917 (pt0) REVERT: p 601 VAL cc_start: 0.8526 (t) cc_final: 0.8147 (t) REVERT: p 630 LYS cc_start: 0.6864 (mttt) cc_final: 0.6534 (mttm) REVERT: p 641 ASP cc_start: 0.6798 (m-30) cc_final: 0.6562 (m-30) REVERT: p 683 GLN cc_start: 0.7860 (mm110) cc_final: 0.7201 (mm-40) REVERT: p 745 ASP cc_start: 0.7310 (m-30) cc_final: 0.7088 (m-30) REVERT: p 747 LEU cc_start: 0.8071 (mt) cc_final: 0.7697 (mp) REVERT: p 796 MET cc_start: 0.8477 (mtm) cc_final: 0.8243 (ttm) REVERT: p 802 ASP cc_start: 0.6741 (m-30) cc_final: 0.6300 (m-30) REVERT: p 952 GLU cc_start: 0.7301 (pt0) cc_final: 0.6989 (pm20) REVERT: p 958 CYS cc_start: 0.8269 (p) cc_final: 0.7965 (p) REVERT: p 1080 ARG cc_start: 0.7842 (mtt90) cc_final: 0.7176 (mtp85) REVERT: p 1106 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6706 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8210 (mt) cc_final: 0.7898 (mt) REVERT: p 1143 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6391 (tttp) REVERT: q 6 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: q 17 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7535 (tt0) REVERT: q 83 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7422 (mt0) REVERT: q 111 GLN cc_start: 0.7890 (tt0) cc_final: 0.7609 (mp10) REVERT: q 126 ARG cc_start: 0.7424 (mtt180) cc_final: 0.6953 (mmm-85) REVERT: q 185 GLU cc_start: 0.8239 (tt0) cc_final: 0.7664 (tt0) REVERT: s 99 ILE cc_start: 0.7922 (mt) cc_final: 0.7594 (mm) REVERT: s 117 SER cc_start: 0.8250 (t) cc_final: 0.8002 (p) REVERT: s 159 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7524 (tp) REVERT: s 191 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7936 (p) REVERT: s 210 GLN cc_start: 0.6413 (mt0) cc_final: 0.5950 (tm-30) REVERT: t 82 GLU cc_start: 0.8587 (pm20) cc_final: 0.8273 (pm20) REVERT: t 86 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7506 (mt-10) REVERT: v 23 ASP cc_start: 0.7664 (m-30) cc_final: 0.7274 (m-30) REVERT: v 28 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6502 (mt) REVERT: v 31 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5294 (tm-30) REVERT: v 95 LYS cc_start: 0.6649 (tttt) cc_final: 0.6339 (ttmt) REVERT: v 100 GLU cc_start: 0.6989 (tt0) cc_final: 0.6448 (mm-30) REVERT: w 15 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7455 (pmm-80) REVERT: w 82 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: x 62 TYR cc_start: 0.8101 (m-80) cc_final: 0.7871 (m-80) REVERT: y 23 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7343 (tttm) REVERT: y 26 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7762 (mtmp) REVERT: y 48 SER cc_start: 0.8035 (t) cc_final: 0.7764 (p) REVERT: y 70 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8141 (ttmm) REVERT: z 56 ASP cc_start: 0.7029 (m-30) cc_final: 0.6531 (p0) outliers start: 177 outliers final: 91 residues processed: 670 average time/residue: 1.4984 time to fit residues: 1208.3140 Evaluate side-chains 661 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 543 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 106 VAL Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 516 GLN Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 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 725 LEU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 902 GLU Chi-restraints excluded: chain o residue 959 MET Chi-restraints excluded: chain o residue 977 VAL Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1226 LEU Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1332 GLN Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 159 THR Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 193 VAL Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 240 LEU Chi-restraints excluded: chain p residue 265 GLN Chi-restraints excluded: chain p residue 294 ASP Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 541 ILE Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 598 VAL Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 638 ARG Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 815 LYS Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1143 LYS Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 191 VAL Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 95 LYS Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain u residue 157 ILE Chi-restraints excluded: chain v residue 25 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 31 GLU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 26 LYS Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain y residue 110 LYS Chi-restraints excluded: chain z residue 52 LEU 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: 3.9990 chunk 231 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 347 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 136 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 926 ASN o 947 HIS o1360 ASN ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 718 GLN p 790 GLN ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN w 46 GLN w 50 ASN w 91 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36635 Z= 0.299 Angle : 0.505 10.222 49969 Z= 0.266 Chirality : 0.041 0.169 5568 Planarity : 0.004 0.063 6099 Dihedral : 16.468 116.101 5822 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 30.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.83 % Favored : 94.97 % Rotamer: Outliers : 5.64 % Allowed : 18.87 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.13), residues: 4137 helix: 1.75 (0.14), residues: 1411 sheet: 0.18 (0.19), residues: 677 loop : -0.23 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP o1192 HIS 0.015 0.001 HIS r 43 PHE 0.013 0.001 PHE p 364 TYR 0.014 0.002 TYR z 17 ARG 0.008 0.000 ARG u 63 *********************** 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 760 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 552 time to evaluate : 4.391 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: o 16 ARG cc_start: 0.7289 (mmt90) cc_final: 0.6861 (mmt90) REVERT: o 37 THR cc_start: 0.7773 (m) cc_final: 0.7213 (p) REVERT: o 38 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7704 (mt-10) REVERT: o 45 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6582 (pm20) REVERT: o 61 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6594 (ptm160) REVERT: o 112 PHE cc_start: 0.7730 (t80) cc_final: 0.7445 (t80) REVERT: o 246 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: o 291 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6968 (ttp80) REVERT: o 305 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7090 (tm-30) REVERT: o 329 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6902 (ttp) REVERT: o 425 ASP cc_start: 0.6641 (m-30) cc_final: 0.5901 (p0) REVERT: o 426 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.7012 (mtm-85) REVERT: o 524 MET cc_start: 0.7872 (mmp) cc_final: 0.7306 (mmm) REVERT: o 612 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7064 (p0) REVERT: o 683 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6480 (tt0) REVERT: o 712 ASP cc_start: 0.6656 (m-30) cc_final: 0.6394 (m-30) REVERT: o 725 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8073 (tt) REVERT: o 818 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7215 (pm20) REVERT: o 868 MET cc_start: 0.7145 (ptt) cc_final: 0.6899 (ptt) REVERT: o 872 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7535 (ttm) REVERT: o 876 ASP cc_start: 0.7854 (t0) cc_final: 0.7287 (t0) REVERT: o 902 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7179 (pt0) REVERT: o 945 ASN cc_start: 0.7269 (t0) cc_final: 0.6980 (t0) REVERT: o 976 LYS cc_start: 0.7728 (ttmt) cc_final: 0.7059 (tptt) REVERT: o 1063 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7041 (mp0) REVERT: o 1085 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7010 (mt-10) REVERT: o 1132 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8358 (mppt) REVERT: o 1168 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7898 (mttp) REVERT: o 1269 MET cc_start: 0.3995 (OUTLIER) cc_final: 0.3502 (pmm) REVERT: o 1306 LYS cc_start: 0.6825 (mttt) cc_final: 0.6284 (mmmt) REVERT: o 1332 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: o 1339 ASP cc_start: 0.6682 (t0) cc_final: 0.6457 (m-30) REVERT: o 1383 TYR cc_start: 0.7416 (t80) cc_final: 0.7177 (t80) REVERT: o 1391 SER cc_start: 0.8062 (t) cc_final: 0.7509 (p) REVERT: o 1423 ASP cc_start: 0.7634 (m-30) cc_final: 0.6826 (t0) REVERT: p 17 ILE cc_start: 0.9057 (mt) cc_final: 0.8694 (mm) REVERT: p 90 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.5979 (tt0) REVERT: p 109 MET cc_start: 0.6973 (mmm) cc_final: 0.6609 (mmm) REVERT: p 152 ILE cc_start: 0.7784 (mt) cc_final: 0.7578 (mm) REVERT: p 168 ASP cc_start: 0.6791 (p0) cc_final: 0.6536 (m-30) REVERT: p 193 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7524 (p) REVERT: p 233 SER cc_start: 0.6886 (t) cc_final: 0.6596 (p) REVERT: p 290 TYR cc_start: 0.7565 (m-80) cc_final: 0.7219 (m-80) REVERT: p 335 ARG cc_start: 0.6731 (mtm180) cc_final: 0.6382 (mtm-85) REVERT: p 381 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7719 (mp0) REVERT: p 386 ASP cc_start: 0.6668 (m-30) cc_final: 0.6294 (m-30) REVERT: p 388 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: p 414 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5165 (mp0) REVERT: p 442 ASP cc_start: 0.6276 (m-30) cc_final: 0.5957 (m-30) REVERT: p 471 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7666 (t0) REVERT: p 597 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7886 (mp) REVERT: p 600 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6808 (pt0) REVERT: p 601 VAL cc_start: 0.8496 (t) cc_final: 0.8137 (t) REVERT: p 606 ASP cc_start: 0.6272 (t0) cc_final: 0.5941 (t0) REVERT: p 641 ASP cc_start: 0.6868 (m-30) cc_final: 0.6653 (m-30) REVERT: p 683 GLN cc_start: 0.7781 (mm110) cc_final: 0.7159 (mm-40) REVERT: p 747 LEU cc_start: 0.8002 (mt) cc_final: 0.7717 (mp) REVERT: p 796 MET cc_start: 0.8400 (mtm) cc_final: 0.8161 (ttm) REVERT: p 802 ASP cc_start: 0.6704 (m-30) cc_final: 0.6175 (m-30) REVERT: p 952 GLU cc_start: 0.7363 (pt0) cc_final: 0.7016 (pm20) REVERT: p 958 CYS cc_start: 0.8324 (p) cc_final: 0.7975 (p) REVERT: p 1080 ARG cc_start: 0.7690 (mtt90) cc_final: 0.7011 (mtp85) REVERT: p 1106 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6799 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8215 (mt) cc_final: 0.7960 (mt) REVERT: p 1131 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.8401 (mtp85) REVERT: p 1138 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.5044 (mmt90) REVERT: p 1143 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6581 (tttp) REVERT: q 6 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: q 17 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7641 (tt0) REVERT: q 44 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6520 (tt) REVERT: q 83 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: q 111 GLN cc_start: 0.7930 (tt0) cc_final: 0.7638 (mp10) REVERT: q 126 ARG cc_start: 0.7425 (mtt180) cc_final: 0.6939 (mmm-85) REVERT: q 185 GLU cc_start: 0.8189 (tt0) cc_final: 0.7530 (tt0) REVERT: s 72 MET cc_start: 0.8924 (ttp) cc_final: 0.8442 (ttm) REVERT: s 117 SER cc_start: 0.8311 (t) cc_final: 0.8035 (p) REVERT: s 159 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7602 (tp) REVERT: s 191 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7929 (p) REVERT: s 210 GLN cc_start: 0.6372 (mt0) cc_final: 0.5895 (tm-30) REVERT: t 82 GLU cc_start: 0.8855 (pm20) cc_final: 0.8590 (pm20) REVERT: t 86 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7569 (mt-10) REVERT: u 1 MET cc_start: 0.8084 (tpp) cc_final: 0.7747 (tmm) REVERT: v 14 ASP cc_start: 0.6226 (m-30) cc_final: 0.5988 (m-30) REVERT: v 23 ASP cc_start: 0.7677 (m-30) cc_final: 0.7327 (m-30) REVERT: v 28 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6495 (mt) REVERT: v 95 LYS cc_start: 0.6702 (tttt) cc_final: 0.6375 (ttmt) REVERT: v 100 GLU cc_start: 0.7447 (tt0) cc_final: 0.6815 (mm-30) REVERT: v 103 GLU cc_start: 0.8138 (pm20) cc_final: 0.7890 (pm20) REVERT: w 15 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7428 (pmm-80) REVERT: w 74 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6975 (mt0) REVERT: w 82 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: y 23 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7352 (tttm) REVERT: y 26 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7683 (mtmp) REVERT: y 48 SER cc_start: 0.8073 (t) cc_final: 0.7786 (p) REVERT: y 70 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8035 (ttmm) REVERT: z 15 MET cc_start: 0.5485 (mmt) cc_final: 0.5236 (mpt) REVERT: z 56 ASP cc_start: 0.6925 (m-30) cc_final: 0.6514 (p0) outliers start: 208 outliers final: 113 residues processed: 678 average time/residue: 1.5016 time to fit residues: 1226.6877 Evaluate side-chains 682 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 538 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 106 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 253 LEU Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 508 SER Chi-restraints excluded: chain o residue 516 GLN Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 682 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 725 LEU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 847 LEU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 902 GLU Chi-restraints excluded: chain o residue 977 VAL Chi-restraints excluded: chain o residue 1021 VAL Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1332 GLN Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1400 LEU Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 53 MET Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 159 THR Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 193 VAL Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 240 LEU Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 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 537 GLN Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 815 LYS Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1138 ARG Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain p residue 1143 LYS Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 191 VAL Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain u residue 157 ILE Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain v residue 25 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 31 GLU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 143 LEU Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 74 GLN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 26 LYS Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain y residue 110 LYS Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 52 LEU 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: 3.9990 chunk 366 optimal weight: 30.0000 chunk 80 optimal weight: 0.9990 chunk 238 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 407 optimal weight: 0.9980 chunk 338 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 136 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 926 ASN o 947 HIS o 950 ASN ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p1007 ASN p1133 HIS q 157 GLN ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN w 46 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36635 Z= 0.343 Angle : 0.527 9.958 49969 Z= 0.278 Chirality : 0.042 0.196 5568 Planarity : 0.004 0.062 6099 Dihedral : 16.472 118.223 5822 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.05 % Favored : 94.75 % Rotamer: Outliers : 5.80 % Allowed : 18.95 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.13), residues: 4137 helix: 1.67 (0.14), residues: 1402 sheet: 0.12 (0.19), residues: 690 loop : -0.30 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP o1192 HIS 0.012 0.001 HIS r 43 PHE 0.017 0.002 PHE o 397 TYR 0.016 0.002 TYR p1048 ARG 0.010 0.001 ARG w 40 *********************** 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 759 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 545 time to evaluate : 4.229 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: o 16 ARG cc_start: 0.7334 (mmt90) cc_final: 0.6876 (mmt90) REVERT: o 37 THR cc_start: 0.7862 (m) cc_final: 0.7271 (p) REVERT: o 38 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7765 (mt-10) REVERT: o 45 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: o 61 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6583 (ptm160) REVERT: o 112 PHE cc_start: 0.7618 (t80) cc_final: 0.7402 (t80) REVERT: o 116 LYS cc_start: 0.8301 (mttt) cc_final: 0.8085 (mtpt) REVERT: o 187 TYR cc_start: 0.8002 (m-10) cc_final: 0.7802 (m-10) REVERT: o 192 ARG cc_start: 0.7130 (mtp-110) cc_final: 0.6693 (ptm160) REVERT: o 246 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6497 (pm20) REVERT: o 291 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6984 (ttp80) REVERT: o 305 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7285 (tm-30) REVERT: o 329 MET cc_start: 0.7984 (mtp) cc_final: 0.7454 (mtp) REVERT: o 342 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5013 (mtm180) REVERT: o 426 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7072 (mtm-85) REVERT: o 524 MET cc_start: 0.7870 (mmp) cc_final: 0.7314 (mmm) REVERT: o 612 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7540 (p0) REVERT: o 683 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6422 (tt0) REVERT: o 712 ASP cc_start: 0.6656 (m-30) cc_final: 0.6398 (m-30) REVERT: o 725 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8098 (tt) REVERT: o 818 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7077 (pm20) REVERT: o 845 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: o 872 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7562 (ttm) REVERT: o 876 ASP cc_start: 0.8013 (t0) cc_final: 0.7426 (t0) REVERT: o 902 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: o 945 ASN cc_start: 0.7286 (t0) cc_final: 0.7045 (t0) REVERT: o 953 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7829 (mm-30) REVERT: o 976 LYS cc_start: 0.7762 (ttmt) cc_final: 0.7073 (tptt) REVERT: o 1063 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7034 (mp0) REVERT: o 1132 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8328 (mppt) REVERT: o 1168 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7830 (mttp) REVERT: o 1254 LYS cc_start: 0.8195 (mtpm) cc_final: 0.7881 (mtpp) REVERT: o 1269 MET cc_start: 0.3256 (OUTLIER) cc_final: 0.2653 (pmm) REVERT: o 1306 LYS cc_start: 0.6831 (mttt) cc_final: 0.6360 (mmmt) REVERT: o 1423 ASP cc_start: 0.7577 (m-30) cc_final: 0.6747 (t0) REVERT: p 17 ILE cc_start: 0.9074 (mt) cc_final: 0.8729 (mm) REVERT: p 90 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.5962 (tt0) REVERT: p 109 MET cc_start: 0.6947 (mmm) cc_final: 0.6606 (mmm) REVERT: p 193 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7506 (p) REVERT: p 233 SER cc_start: 0.6894 (t) cc_final: 0.6650 (p) REVERT: p 255 ARG cc_start: 0.6175 (mtm110) cc_final: 0.5709 (mtm-85) REVERT: p 335 ARG cc_start: 0.6697 (mtm180) cc_final: 0.6488 (mtm-85) REVERT: p 381 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7712 (mp0) REVERT: p 386 ASP cc_start: 0.6660 (m-30) cc_final: 0.6165 (m-30) REVERT: p 388 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: p 414 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5139 (mp0) REVERT: p 442 ASP cc_start: 0.6332 (m-30) cc_final: 0.6012 (m-30) REVERT: p 551 GLU cc_start: 0.7470 (mp0) cc_final: 0.7115 (mp0) REVERT: p 597 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7876 (mp) REVERT: p 600 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6814 (pt0) REVERT: p 601 VAL cc_start: 0.8487 (t) cc_final: 0.8107 (t) REVERT: p 606 ASP cc_start: 0.6334 (t0) cc_final: 0.6011 (t0) REVERT: p 683 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7294 (mm-40) REVERT: p 747 LEU cc_start: 0.8037 (mt) cc_final: 0.7730 (mp) REVERT: p 802 ASP cc_start: 0.6785 (m-30) cc_final: 0.6444 (m-30) REVERT: p 942 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7124 (pttt) REVERT: p 952 GLU cc_start: 0.7387 (pt0) cc_final: 0.7019 (pm20) REVERT: p 958 CYS cc_start: 0.8388 (p) cc_final: 0.7997 (p) REVERT: p 1080 ARG cc_start: 0.7686 (mtt90) cc_final: 0.7002 (mtp85) REVERT: p 1106 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6978 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8180 (mt) cc_final: 0.7848 (mt) REVERT: p 1131 ARG cc_start: 0.8658 (mtt-85) cc_final: 0.8353 (mtp85) REVERT: p 1138 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.5152 (mmt90) REVERT: p 1143 LYS cc_start: 0.6816 (tttp) cc_final: 0.6605 (tttp) REVERT: q 6 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: q 17 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7666 (tt0) REVERT: q 44 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6524 (tt) REVERT: q 83 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: q 126 ARG cc_start: 0.7372 (mtt180) cc_final: 0.6893 (mmm-85) REVERT: q 185 GLU cc_start: 0.8157 (tt0) cc_final: 0.7602 (tt0) REVERT: s 26 TYR cc_start: 0.8118 (m-80) cc_final: 0.7910 (m-80) REVERT: s 108 GLN cc_start: 0.8236 (mt0) cc_final: 0.8005 (mt0) REVERT: s 159 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7435 (tp) REVERT: s 187 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7423 (ttm110) REVERT: s 191 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7958 (p) REVERT: s 210 GLN cc_start: 0.6354 (mt0) cc_final: 0.5843 (tm-30) REVERT: t 82 GLU cc_start: 0.8886 (pm20) cc_final: 0.8618 (pm20) REVERT: t 86 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7631 (mt-10) REVERT: t 101 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.5731 (mptp) REVERT: t 112 ASP cc_start: 0.8362 (p0) cc_final: 0.8067 (p0) REVERT: t 114 SER cc_start: 0.7450 (t) cc_final: 0.6889 (p) REVERT: u 111 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7956 (p-80) REVERT: u 120 ASP cc_start: 0.4448 (m-30) cc_final: 0.3450 (p0) REVERT: u 164 MET cc_start: 0.5411 (mmt) cc_final: 0.5111 (mpt) REVERT: v 14 ASP cc_start: 0.6294 (m-30) cc_final: 0.5822 (t0) REVERT: v 23 ASP cc_start: 0.7718 (m-30) cc_final: 0.7368 (m-30) REVERT: v 28 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6591 (mt) REVERT: v 95 LYS cc_start: 0.6760 (tttt) cc_final: 0.6393 (ttmt) REVERT: v 100 GLU cc_start: 0.7343 (tt0) cc_final: 0.6764 (mm-30) REVERT: v 141 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7386 (p) REVERT: w 15 ARG cc_start: 0.7836 (ptp90) cc_final: 0.7419 (pmm-80) REVERT: w 25 TYR cc_start: 0.6815 (m-80) cc_final: 0.6602 (m-80) REVERT: w 40 ARG cc_start: 0.7174 (mmt180) cc_final: 0.6789 (mmt180) REVERT: w 74 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6963 (mt0) REVERT: w 82 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: x 62 TYR cc_start: 0.8119 (m-80) cc_final: 0.7896 (m-80) REVERT: y 23 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7424 (tttm) REVERT: y 26 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7682 (mtmp) REVERT: y 48 SER cc_start: 0.8100 (t) cc_final: 0.7808 (p) REVERT: y 68 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6491 (mp0) REVERT: y 70 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8064 (ttmm) REVERT: z 46 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7194 (tptt) REVERT: z 56 ASP cc_start: 0.6949 (m-30) cc_final: 0.6452 (p0) outliers start: 214 outliers final: 125 residues processed: 679 average time/residue: 1.5050 time to fit residues: 1226.1327 Evaluate side-chains 689 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 528 time to evaluate : 6.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 106 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 193 ARG Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 253 LEU Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 342 ARG Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 508 SER Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 682 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 725 LEU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 803 LYS Chi-restraints excluded: chain o residue 845 GLU Chi-restraints excluded: chain o residue 847 LEU Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 902 GLU Chi-restraints excluded: chain o residue 977 VAL Chi-restraints excluded: chain o residue 1021 VAL Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1144 LEU Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1269 MET Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1367 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1400 LEU Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 53 MET Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 90 GLN Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 159 THR Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 193 VAL Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 239 MET Chi-restraints excluded: chain p residue 240 LEU Chi-restraints excluded: chain p residue 294 ASP Chi-restraints excluded: chain p residue 345 LYS Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 421 LYS Chi-restraints excluded: chain p residue 435 ILE Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 537 GLN Chi-restraints excluded: chain p residue 541 ILE Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 582 GLN Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 683 GLN Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 923 VAL Chi-restraints excluded: chain p residue 931 ILE Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1069 ILE Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1133 HIS Chi-restraints excluded: chain p residue 1138 ARG Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain q residue 6 GLN Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 13 ILE Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 187 ARG Chi-restraints excluded: chain s residue 191 VAL Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 101 LYS Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 157 ILE Chi-restraints excluded: chain v residue 25 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 31 GLU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 87 GLN 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 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 74 GLN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 26 LYS Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain z residue 46 LYS Chi-restraints excluded: chain z residue 52 LEU 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: 7.9990 chunk 45 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 247 optimal weight: 0.9990 chunk 187 optimal weight: 0.2980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 77 ASN o 136 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 947 HIS ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1007 ASN p1133 HIS ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN t 46 GLN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 4 HIS ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN ** w 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 84 HIS w 98 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36635 Z= 0.203 Angle : 0.464 9.681 49969 Z= 0.246 Chirality : 0.040 0.170 5568 Planarity : 0.003 0.062 6099 Dihedral : 16.393 118.502 5822 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 4.77 % Allowed : 20.47 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4137 helix: 1.88 (0.14), residues: 1402 sheet: 0.19 (0.19), residues: 678 loop : -0.24 (0.14), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP o1192 HIS 0.018 0.001 HIS p1133 PHE 0.011 0.001 PHE y 13 TYR 0.015 0.001 TYR r 67 ARG 0.009 0.000 ARG u 63 *********************** 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 723 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 547 time to evaluate : 4.173 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: o 16 ARG cc_start: 0.7322 (mmt90) cc_final: 0.6783 (mmt90) REVERT: o 37 THR cc_start: 0.7830 (m) cc_final: 0.7253 (p) REVERT: o 38 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7835 (mt-10) REVERT: o 45 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: o 61 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6606 (ptm160) REVERT: o 112 PHE cc_start: 0.7492 (t80) cc_final: 0.7282 (t80) REVERT: o 116 LYS cc_start: 0.8226 (mttt) cc_final: 0.8003 (mtpt) REVERT: o 151 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6814 (mtpp) REVERT: o 187 TYR cc_start: 0.7992 (m-10) cc_final: 0.7788 (m-10) REVERT: o 246 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6457 (pm20) REVERT: o 305 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7165 (tm-30) REVERT: o 329 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: o 426 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7080 (mtm-85) REVERT: o 524 MET cc_start: 0.7872 (mmp) cc_final: 0.7303 (mmm) REVERT: o 612 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7549 (p0) REVERT: o 683 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: o 712 ASP cc_start: 0.6634 (m-30) cc_final: 0.6362 (m-30) REVERT: o 725 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8104 (tt) REVERT: o 818 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7079 (pm20) REVERT: o 872 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7534 (ttm) REVERT: o 876 ASP cc_start: 0.7991 (t0) cc_final: 0.7396 (t0) REVERT: o 902 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7151 (pt0) REVERT: o 945 ASN cc_start: 0.7277 (t0) cc_final: 0.7049 (t0) REVERT: o 953 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7822 (mm-30) REVERT: o 976 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7072 (tptt) REVERT: o 1063 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7222 (mp0) REVERT: o 1132 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8320 (mppt) REVERT: o 1168 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7854 (mttp) REVERT: o 1218 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8483 (mmm-85) REVERT: o 1254 LYS cc_start: 0.8088 (mtpm) cc_final: 0.7840 (mtpp) REVERT: o 1269 MET cc_start: 0.3281 (pmt) cc_final: 0.2664 (pmm) REVERT: o 1302 GLU cc_start: 0.8015 (mp0) cc_final: 0.7786 (tt0) REVERT: o 1306 LYS cc_start: 0.6779 (mttt) cc_final: 0.6282 (mmmt) REVERT: o 1423 ASP cc_start: 0.7586 (m-30) cc_final: 0.6731 (t0) REVERT: p 17 ILE cc_start: 0.9070 (mt) cc_final: 0.8718 (mm) REVERT: p 109 MET cc_start: 0.7002 (mmm) cc_final: 0.6615 (mmm) REVERT: p 193 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7563 (p) REVERT: p 233 SER cc_start: 0.6833 (t) cc_final: 0.6578 (p) REVERT: p 266 GLU cc_start: 0.7440 (pp20) cc_final: 0.7115 (pp20) REVERT: p 381 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7708 (mp0) REVERT: p 386 ASP cc_start: 0.6664 (m-30) cc_final: 0.6152 (m-30) REVERT: p 388 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: p 414 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.5111 (mp0) REVERT: p 442 ASP cc_start: 0.6296 (m-30) cc_final: 0.5976 (m-30) REVERT: p 597 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7893 (mp) REVERT: p 600 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6809 (pt0) REVERT: p 601 VAL cc_start: 0.8366 (t) cc_final: 0.7994 (t) REVERT: p 606 ASP cc_start: 0.6321 (t0) cc_final: 0.5950 (t0) REVERT: p 683 GLN cc_start: 0.7702 (mm110) cc_final: 0.7290 (mm-40) REVERT: p 747 LEU cc_start: 0.8022 (mt) cc_final: 0.7738 (mp) REVERT: p 802 ASP cc_start: 0.6988 (m-30) cc_final: 0.6592 (m-30) REVERT: p 952 GLU cc_start: 0.7339 (pt0) cc_final: 0.6950 (pm20) REVERT: p 958 CYS cc_start: 0.8381 (p) cc_final: 0.8024 (p) REVERT: p 1080 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7250 (mtp85) REVERT: p 1106 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6913 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8164 (mt) cc_final: 0.7857 (mt) REVERT: p 1131 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8345 (mtp85) REVERT: p 1143 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.6573 (tttp) REVERT: q 17 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7654 (tt0) REVERT: q 44 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6308 (tt) REVERT: q 83 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: q 126 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6898 (mmm-85) REVERT: q 185 GLU cc_start: 0.8127 (tt0) cc_final: 0.7619 (tt0) REVERT: s 26 TYR cc_start: 0.8128 (m-80) cc_final: 0.7909 (m-80) REVERT: s 61 LEU cc_start: 0.8855 (tp) cc_final: 0.8548 (tm) REVERT: s 108 GLN cc_start: 0.8206 (mt0) cc_final: 0.7977 (mt0) REVERT: s 210 GLN cc_start: 0.6369 (mt0) cc_final: 0.5896 (tm-30) REVERT: t 82 GLU cc_start: 0.8880 (pm20) cc_final: 0.8652 (pm20) REVERT: t 86 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7771 (mt-10) REVERT: t 112 ASP cc_start: 0.8386 (p0) cc_final: 0.8138 (p0) REVERT: t 114 SER cc_start: 0.7446 (t) cc_final: 0.6948 (p) REVERT: u 120 ASP cc_start: 0.4491 (m-30) cc_final: 0.3441 (p0) REVERT: u 164 MET cc_start: 0.5410 (mmt) cc_final: 0.4988 (mmt) REVERT: v 14 ASP cc_start: 0.6524 (m-30) cc_final: 0.6031 (t0) REVERT: v 23 ASP cc_start: 0.7717 (m-30) cc_final: 0.7378 (m-30) REVERT: v 95 LYS cc_start: 0.6666 (tttt) cc_final: 0.6396 (ttmt) REVERT: v 100 GLU cc_start: 0.7348 (tt0) cc_final: 0.6766 (mm-30) REVERT: v 141 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7393 (p) REVERT: w 15 ARG cc_start: 0.7821 (ptp90) cc_final: 0.7385 (pmm-80) REVERT: w 82 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: y 23 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7429 (tttm) REVERT: y 26 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (mtmp) REVERT: y 48 SER cc_start: 0.8067 (t) cc_final: 0.7783 (p) REVERT: y 68 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6480 (mp0) REVERT: y 70 LYS cc_start: 0.8350 (ttpt) cc_final: 0.8017 (ttmm) REVERT: z 56 ASP cc_start: 0.6999 (m-30) cc_final: 0.6460 (p0) outliers start: 176 outliers final: 105 residues processed: 649 average time/residue: 1.5188 time to fit residues: 1182.9751 Evaluate side-chains 663 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 535 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 94 VAL Chi-restraints excluded: chain o residue 106 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 151 LYS Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 516 GLN Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 682 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 725 LEU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 902 GLU Chi-restraints excluded: chain o residue 947 HIS Chi-restraints excluded: chain o residue 977 VAL Chi-restraints excluded: chain o residue 1021 VAL Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1234 LYS Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1400 LEU Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1422 GLN Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain o residue 1451 MET Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 193 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 345 LYS Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 421 LYS Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 537 GLN Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 650 ASN Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1131 ARG Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain p residue 1143 LYS Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain p residue 1172 MET Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain v residue 25 VAL Chi-restraints excluded: chain v residue 31 GLU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain v residue 141 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 23 MET Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 26 LYS Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain z residue 52 LEU 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: 0.0980 chunk 162 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 318 optimal weight: 30.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 77 ASN o 136 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 861 GLN o 947 HIS ** p 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1007 ASN p1133 HIS ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN t 46 GLN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN v 126 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36635 Z= 0.275 Angle : 0.488 9.809 49969 Z= 0.258 Chirality : 0.040 0.168 5568 Planarity : 0.004 0.060 6099 Dihedral : 16.344 119.207 5822 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.12 % Favored : 94.68 % Rotamer: Outliers : 4.96 % Allowed : 20.61 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4137 helix: 1.85 (0.14), residues: 1402 sheet: 0.13 (0.20), residues: 676 loop : -0.28 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP o1192 HIS 0.025 0.001 HIS o 947 PHE 0.015 0.001 PHE o 397 TYR 0.018 0.001 TYR t 115 ARG 0.010 0.000 ARG u 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 535 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.7342 (mmt90) cc_final: 0.6936 (mmt90) REVERT: o 37 THR cc_start: 0.7857 (m) cc_final: 0.7283 (p) REVERT: o 38 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7817 (mt-10) REVERT: o 45 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6569 (pm20) REVERT: o 61 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6561 (ptm160) REVERT: o 112 PHE cc_start: 0.7525 (t80) cc_final: 0.7319 (t80) REVERT: o 116 LYS cc_start: 0.8156 (mttt) cc_final: 0.7880 (mttt) REVERT: o 151 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6854 (mtpp) REVERT: o 192 ARG cc_start: 0.6976 (mtm110) cc_final: 0.6692 (mtm110) REVERT: o 246 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6521 (pm20) REVERT: o 291 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6939 (ttp80) REVERT: o 305 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7177 (tm-30) REVERT: o 329 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7462 (mtp) REVERT: o 426 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7095 (mtm-85) REVERT: o 524 MET cc_start: 0.7878 (mmp) cc_final: 0.7299 (mmm) REVERT: o 612 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7598 (p0) REVERT: o 683 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: o 712 ASP cc_start: 0.6648 (m-30) cc_final: 0.6381 (m-30) REVERT: o 725 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8111 (tt) REVERT: o 818 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7089 (pm20) REVERT: o 872 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7550 (ttm) REVERT: o 876 ASP cc_start: 0.8026 (t0) cc_final: 0.7433 (t0) REVERT: o 902 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: o 945 ASN cc_start: 0.7394 (t0) cc_final: 0.7107 (t0) REVERT: o 953 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7821 (mm-30) REVERT: o 976 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7067 (tptt) REVERT: o 1063 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7228 (mp0) REVERT: o 1132 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8333 (mppt) REVERT: o 1168 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7956 (mttp) REVERT: o 1254 LYS cc_start: 0.8144 (mtpm) cc_final: 0.7904 (mtpp) REVERT: o 1269 MET cc_start: 0.3327 (pmt) cc_final: 0.2722 (pmm) REVERT: o 1302 GLU cc_start: 0.8007 (mp0) cc_final: 0.7785 (tt0) REVERT: o 1306 LYS cc_start: 0.6783 (mttt) cc_final: 0.6283 (mmmt) REVERT: o 1351 ASP cc_start: 0.8096 (m-30) cc_final: 0.7576 (m-30) REVERT: o 1423 ASP cc_start: 0.7608 (m-30) cc_final: 0.6748 (t0) REVERT: p 17 ILE cc_start: 0.9166 (mt) cc_final: 0.8808 (mm) REVERT: p 109 MET cc_start: 0.7004 (mmm) cc_final: 0.6620 (mmm) REVERT: p 193 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7539 (p) REVERT: p 233 SER cc_start: 0.6890 (t) cc_final: 0.6652 (p) REVERT: p 255 ARG cc_start: 0.6097 (mtm110) cc_final: 0.5609 (mtm-85) REVERT: p 381 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7686 (mp0) REVERT: p 386 ASP cc_start: 0.6686 (m-30) cc_final: 0.6147 (m-30) REVERT: p 388 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: p 414 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.5109 (mp0) REVERT: p 551 GLU cc_start: 0.7460 (mp0) cc_final: 0.7060 (mp0) REVERT: p 597 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7843 (mp) REVERT: p 600 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6819 (pt0) REVERT: p 601 VAL cc_start: 0.8381 (t) cc_final: 0.8014 (t) REVERT: p 606 ASP cc_start: 0.6351 (t0) cc_final: 0.5999 (t0) REVERT: p 683 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: p 747 LEU cc_start: 0.7972 (mt) cc_final: 0.7688 (mp) REVERT: p 802 ASP cc_start: 0.6936 (m-30) cc_final: 0.6567 (m-30) REVERT: p 942 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7087 (pttt) REVERT: p 952 GLU cc_start: 0.7405 (pt0) cc_final: 0.7035 (pm20) REVERT: p 958 CYS cc_start: 0.8392 (p) cc_final: 0.7985 (p) REVERT: p 1080 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7273 (mtp85) REVERT: p 1106 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6909 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8165 (mt) cc_final: 0.7861 (mt) REVERT: p 1131 ARG cc_start: 0.8708 (mtt-85) cc_final: 0.8388 (mtp85) REVERT: p 1138 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5020 (mmt90) REVERT: p 1143 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6568 (tttp) REVERT: q 17 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7460 (tt0) REVERT: q 44 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6343 (tt) REVERT: q 83 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: q 126 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6903 (mmm-85) REVERT: q 185 GLU cc_start: 0.8263 (tt0) cc_final: 0.7681 (tt0) REVERT: s 26 TYR cc_start: 0.8155 (m-80) cc_final: 0.7925 (m-80) REVERT: s 61 LEU cc_start: 0.8838 (tp) cc_final: 0.8531 (tm) REVERT: s 159 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7333 (tp) REVERT: s 191 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.7998 (p) REVERT: s 210 GLN cc_start: 0.6355 (mt0) cc_final: 0.5891 (tm-30) REVERT: t 82 GLU cc_start: 0.8887 (pm20) cc_final: 0.8482 (pm20) REVERT: t 86 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7609 (mt-10) REVERT: t 112 ASP cc_start: 0.8372 (p0) cc_final: 0.8119 (p0) REVERT: t 114 SER cc_start: 0.7463 (t) cc_final: 0.6948 (p) REVERT: u 72 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5957 (p90) REVERT: u 120 ASP cc_start: 0.4441 (m-30) cc_final: 0.3388 (p0) REVERT: u 164 MET cc_start: 0.5412 (mmt) cc_final: 0.4985 (mmt) REVERT: v 14 ASP cc_start: 0.6545 (m-30) cc_final: 0.6054 (t0) REVERT: v 23 ASP cc_start: 0.7728 (m-30) cc_final: 0.7393 (m-30) REVERT: v 95 LYS cc_start: 0.6606 (tttt) cc_final: 0.6390 (ttmt) REVERT: v 100 GLU cc_start: 0.7388 (tt0) cc_final: 0.6796 (mm-30) REVERT: v 141 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7400 (p) REVERT: w 15 ARG cc_start: 0.7937 (ptp90) cc_final: 0.7433 (pmm-80) REVERT: w 27 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7617 (ttmt) REVERT: w 40 ARG cc_start: 0.7067 (mmt180) cc_final: 0.6484 (mmt180) REVERT: w 74 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6776 (mt0) REVERT: w 82 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: y 23 LYS cc_start: 0.8251 (ttpp) cc_final: 0.7432 (tttm) REVERT: y 26 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7644 (mtmp) REVERT: y 48 SER cc_start: 0.8078 (t) cc_final: 0.7789 (p) REVERT: y 70 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8110 (ttmm) REVERT: y 110 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7812 (ptmm) REVERT: z 56 ASP cc_start: 0.6837 (m-30) cc_final: 0.6373 (p0) outliers start: 183 outliers final: 121 residues processed: 647 average time/residue: 1.5374 time to fit residues: 1193.4596 Evaluate side-chains 675 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 524 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 106 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 151 LYS Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 238 MET Chi-restraints excluded: chain o residue 246 GLU Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 503 LEU Chi-restraints excluded: chain o residue 508 SER Chi-restraints excluded: chain o residue 516 GLN Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 621 ILE Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 682 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 725 LEU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 902 GLU Chi-restraints excluded: chain o residue 977 VAL Chi-restraints excluded: chain o residue 1021 VAL Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1234 LYS Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1367 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1400 LEU Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1422 GLN Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 126 VAL Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 159 THR Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 193 VAL Chi-restraints excluded: chain p residue 225 LEU Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 240 LEU Chi-restraints excluded: chain p residue 294 ASP Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 345 LYS Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 421 LYS Chi-restraints excluded: chain p residue 435 ILE Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 537 GLN Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 598 VAL Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 650 ASN Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 683 GLN Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 923 VAL Chi-restraints excluded: chain p residue 931 ILE Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1138 ARG Chi-restraints excluded: chain p residue 1143 LYS Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain p residue 1172 MET Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 80 ASP Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 13 ILE Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 191 VAL Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 72 TYR Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain v residue 25 VAL Chi-restraints excluded: chain v residue 31 GLU Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 45 ILE 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 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 74 GLN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 82 GLU Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 26 LYS Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 52 LEU 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: 4.9990 chunk 388 optimal weight: 1.9990 chunk 354 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 341 optimal weight: 0.7980 chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 77 ASN o 136 GLN o 273 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 28 GLN v 76 ASN v 126 GLN ** w 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36635 Z= 0.349 Angle : 0.530 9.864 49969 Z= 0.278 Chirality : 0.042 0.177 5568 Planarity : 0.004 0.068 6099 Dihedral : 16.295 121.007 5822 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 31.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.25 % Favored : 94.51 % Rotamer: Outliers : 4.99 % Allowed : 20.66 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 4137 helix: 1.68 (0.14), residues: 1401 sheet: 0.03 (0.20), residues: 677 loop : -0.36 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP o1192 HIS 0.010 0.001 HIS p 387 PHE 0.016 0.002 PHE o 397 TYR 0.020 0.002 TYR o 187 ARG 0.011 0.000 ARG u 63 *********************** 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 721 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 537 time to evaluate : 4.210 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: o 16 ARG cc_start: 0.7347 (mmt90) cc_final: 0.6890 (mmt90) REVERT: o 38 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7588 (mm-30) REVERT: o 45 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6586 (pm20) REVERT: o 54 LEU cc_start: 0.7819 (mt) cc_final: 0.7438 (mm) REVERT: o 61 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6502 (ptm160) REVERT: o 116 LYS cc_start: 0.8057 (mttt) cc_final: 0.7668 (mttt) REVERT: o 186 ARG cc_start: 0.7720 (mtt90) cc_final: 0.7497 (mtt90) REVERT: o 192 ARG cc_start: 0.7042 (mtm110) cc_final: 0.6765 (mtm110) REVERT: o 291 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7067 (ttp80) REVERT: o 305 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7166 (tm-30) REVERT: o 329 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7723 (mtp) REVERT: o 342 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.5047 (mtm180) REVERT: o 347 GLU cc_start: 0.7491 (mp0) cc_final: 0.7087 (mp0) REVERT: o 426 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7244 (mtm-85) REVERT: o 524 MET cc_start: 0.7869 (mmp) cc_final: 0.7310 (mmm) REVERT: o 612 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7707 (p0) REVERT: o 683 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6476 (tt0) REVERT: o 712 ASP cc_start: 0.6657 (m-30) cc_final: 0.6396 (m-30) REVERT: o 725 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8146 (tt) REVERT: o 818 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7098 (pm20) REVERT: o 872 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7545 (ttm) REVERT: o 876 ASP cc_start: 0.8089 (t0) cc_final: 0.7475 (t0) REVERT: o 902 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: o 945 ASN cc_start: 0.7396 (t0) cc_final: 0.7131 (t0) REVERT: o 953 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7893 (mm-30) REVERT: o 976 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7092 (tptt) REVERT: o 1054 MET cc_start: 0.8109 (mmt) cc_final: 0.7909 (mmp) REVERT: o 1063 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6991 (mp0) REVERT: o 1132 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8281 (mppt) REVERT: o 1168 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8018 (mttp) REVERT: o 1218 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8482 (mmm-85) REVERT: o 1269 MET cc_start: 0.3442 (pmt) cc_final: 0.2838 (pmm) REVERT: o 1306 LYS cc_start: 0.6796 (mttt) cc_final: 0.6339 (mmmt) REVERT: o 1351 ASP cc_start: 0.8012 (m-30) cc_final: 0.7538 (m-30) REVERT: o 1367 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7513 (p) REVERT: o 1423 ASP cc_start: 0.7664 (m-30) cc_final: 0.6760 (t0) REVERT: p 87 LYS cc_start: 0.6788 (tttt) cc_final: 0.6431 (tptt) REVERT: p 193 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7470 (p) REVERT: p 233 SER cc_start: 0.6940 (t) cc_final: 0.6730 (p) REVERT: p 255 ARG cc_start: 0.6268 (mtm110) cc_final: 0.5751 (mtm-85) REVERT: p 266 GLU cc_start: 0.7523 (pp20) cc_final: 0.7274 (pp20) REVERT: p 335 ARG cc_start: 0.6125 (mtm-85) cc_final: 0.5264 (mtm-85) REVERT: p 381 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7681 (mp0) REVERT: p 386 ASP cc_start: 0.6685 (m-30) cc_final: 0.6116 (m-30) REVERT: p 388 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: p 414 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.5072 (mp0) REVERT: p 442 ASP cc_start: 0.6377 (m-30) cc_final: 0.6021 (m-30) REVERT: p 551 GLU cc_start: 0.7308 (mp0) cc_final: 0.6966 (mp0) REVERT: p 597 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7890 (mp) REVERT: p 600 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6868 (pt0) REVERT: p 601 VAL cc_start: 0.8462 (t) cc_final: 0.8097 (t) REVERT: p 606 ASP cc_start: 0.6349 (t0) cc_final: 0.6040 (t0) REVERT: p 683 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7351 (mm-40) REVERT: p 747 LEU cc_start: 0.8086 (mt) cc_final: 0.7784 (mp) REVERT: p 942 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7126 (pttt) REVERT: p 952 GLU cc_start: 0.7476 (pt0) cc_final: 0.7198 (pm20) REVERT: p 958 CYS cc_start: 0.8408 (p) cc_final: 0.7961 (p) REVERT: p 1080 ARG cc_start: 0.7903 (mtt90) cc_final: 0.7271 (mtp85) REVERT: p 1106 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7032 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8172 (mt) cc_final: 0.7866 (mt) REVERT: p 1131 ARG cc_start: 0.8697 (mtt-85) cc_final: 0.8389 (mtp85) REVERT: p 1138 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.4636 (mmt90) REVERT: p 1143 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6595 (tttp) REVERT: q 44 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6128 (pt) REVERT: q 83 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: q 110 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7448 (t0) REVERT: q 126 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6742 (mmm-85) REVERT: q 185 GLU cc_start: 0.8277 (tt0) cc_final: 0.7771 (tt0) REVERT: s 26 TYR cc_start: 0.8116 (m-80) cc_final: 0.7872 (m-80) REVERT: s 61 LEU cc_start: 0.8847 (tp) cc_final: 0.8544 (tm) REVERT: s 159 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7346 (tp) REVERT: s 191 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7997 (p) REVERT: s 210 GLN cc_start: 0.6292 (mt0) cc_final: 0.5893 (tm-30) REVERT: t 84 GLU cc_start: 0.6600 (pm20) cc_final: 0.6349 (pm20) REVERT: t 86 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7797 (mt-10) REVERT: t 112 ASP cc_start: 0.8363 (p0) cc_final: 0.8100 (p0) REVERT: t 114 SER cc_start: 0.7479 (t) cc_final: 0.7115 (m) REVERT: u 72 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.5841 (p90) REVERT: u 164 MET cc_start: 0.5409 (mmt) cc_final: 0.4988 (mmt) REVERT: v 14 ASP cc_start: 0.6635 (m-30) cc_final: 0.6087 (t0) REVERT: v 23 ASP cc_start: 0.7737 (m-30) cc_final: 0.7396 (m-30) REVERT: v 28 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6638 (mt) REVERT: v 95 LYS cc_start: 0.6647 (tttt) cc_final: 0.6418 (ttmt) REVERT: v 100 GLU cc_start: 0.7404 (tt0) cc_final: 0.6743 (mt-10) REVERT: v 141 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7375 (p) REVERT: w 15 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7288 (pmm-80) REVERT: w 25 TYR cc_start: 0.6888 (m-80) cc_final: 0.6670 (m-80) REVERT: w 40 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6748 (mmt180) REVERT: w 74 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6798 (mt0) REVERT: x 26 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: y 23 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7435 (tttm) REVERT: y 48 SER cc_start: 0.8098 (t) cc_final: 0.7799 (p) REVERT: y 68 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: y 70 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7994 (ttmm) REVERT: y 110 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7778 (ttmm) REVERT: z 56 ASP cc_start: 0.6810 (m-30) cc_final: 0.6288 (p0) outliers start: 184 outliers final: 116 residues processed: 650 average time/residue: 1.5055 time to fit residues: 1173.1404 Evaluate side-chains 679 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 530 time to evaluate : 4.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 106 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 276 LEU Chi-restraints excluded: chain o residue 291 ARG Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 319 ASP Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 342 ARG Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 422 ASP Chi-restraints excluded: chain o residue 487 SER Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 508 SER Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 682 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 725 LEU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 902 GLU Chi-restraints excluded: chain o residue 977 VAL Chi-restraints excluded: chain o residue 1021 VAL Chi-restraints excluded: chain o residue 1104 LEU Chi-restraints excluded: chain o residue 1105 ASN Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1144 LEU Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1168 LYS Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1332 GLN Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1367 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1400 LEU Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain o residue 1441 GLU Chi-restraints excluded: chain o residue 1451 MET Chi-restraints excluded: chain o residue 1470 CYS Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 126 VAL Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 193 VAL Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 240 LEU Chi-restraints excluded: chain p residue 294 ASP Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 345 LYS Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 421 LYS Chi-restraints excluded: chain p residue 435 ILE Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 473 LEU Chi-restraints excluded: chain p residue 569 VAL Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 598 VAL Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 650 ASN Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 683 GLN Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 760 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 909 VAL Chi-restraints excluded: chain p residue 923 VAL Chi-restraints excluded: chain p residue 931 ILE Chi-restraints excluded: chain p residue 942 LYS Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1138 ARG Chi-restraints excluded: chain p residue 1143 LYS Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain p residue 1172 MET Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 110 ASP Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 18 MET Chi-restraints excluded: chain s residue 86 THR Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 191 VAL Chi-restraints excluded: chain s residue 205 THR Chi-restraints excluded: chain t residue 76 CYS Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain t residue 87 THR Chi-restraints excluded: chain t residue 105 ILE Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 72 TYR Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 86 ASP Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 25 VAL Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 31 GLU Chi-restraints excluded: chain v residue 38 ASP 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 141 VAL Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 74 GLN Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 26 GLN Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 68 GLU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain z residue 16 ILE Chi-restraints excluded: chain z residue 52 LEU 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: 0.5980 chunk 399 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 189 optimal weight: 0.0270 chunk 277 optimal weight: 0.9980 chunk 419 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 chunk 333 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 204 optimal weight: 0.1980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 136 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 947 HIS ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 ASN v 76 ASN v 130 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36635 Z= 0.151 Angle : 0.454 9.360 49969 Z= 0.241 Chirality : 0.039 0.168 5568 Planarity : 0.003 0.063 6099 Dihedral : 16.186 120.221 5822 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 32.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.62 % Favored : 95.19 % Rotamer: Outliers : 3.04 % Allowed : 22.80 % Favored : 74.16 % 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: 2.02 (0.15), residues: 1399 sheet: 0.15 (0.20), residues: 660 loop : -0.25 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP o1192 HIS 0.007 0.001 HIS r 43 PHE 0.016 0.001 PHE o 397 TYR 0.018 0.001 TYR t 115 ARG 0.012 0.000 ARG u 63 ********************** 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 664 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 552 time to evaluate : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 16 ARG cc_start: 0.7347 (mmt90) cc_final: 0.6904 (mmt90) REVERT: o 37 THR cc_start: 0.7949 (m) cc_final: 0.7187 (p) REVERT: o 38 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7852 (mm-30) REVERT: o 45 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6418 (pm20) REVERT: o 54 LEU cc_start: 0.7819 (mt) cc_final: 0.7419 (mm) REVERT: o 61 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7134 (ptt180) REVERT: o 116 LYS cc_start: 0.8085 (mttt) cc_final: 0.7761 (mttt) REVERT: o 149 LYS cc_start: 0.7751 (ptpp) cc_final: 0.7261 (ptpp) REVERT: o 186 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7480 (mtt90) REVERT: o 305 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7290 (tm-30) REVERT: o 329 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7735 (mtp) REVERT: o 397 PHE cc_start: 0.7838 (p90) cc_final: 0.7614 (p90) REVERT: o 426 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7150 (mtm-85) REVERT: o 439 HIS cc_start: 0.7813 (m-70) cc_final: 0.7306 (p-80) REVERT: o 524 MET cc_start: 0.7870 (mmp) cc_final: 0.7340 (mmm) REVERT: o 612 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7933 (p0) REVERT: o 683 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6279 (tt0) REVERT: o 712 ASP cc_start: 0.6617 (m-30) cc_final: 0.6332 (m-30) REVERT: o 725 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8150 (tt) REVERT: o 728 THR cc_start: 0.6594 (OUTLIER) cc_final: 0.6158 (p) REVERT: o 733 LEU cc_start: 0.7822 (tp) cc_final: 0.7561 (tm) REVERT: o 818 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7087 (pm20) REVERT: o 872 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7490 (ttm) REVERT: o 876 ASP cc_start: 0.8044 (t0) cc_final: 0.7428 (t0) REVERT: o 945 ASN cc_start: 0.7376 (t0) cc_final: 0.7138 (t0) REVERT: o 953 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7879 (mm-30) REVERT: o 976 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7094 (tptt) REVERT: o 1054 MET cc_start: 0.8063 (mmt) cc_final: 0.7848 (mmp) REVERT: o 1063 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7161 (mp0) REVERT: o 1132 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8310 (mppt) REVERT: o 1218 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8552 (mmm-85) REVERT: o 1269 MET cc_start: 0.3362 (pmt) cc_final: 0.2770 (pmm) REVERT: o 1302 GLU cc_start: 0.8016 (mp0) cc_final: 0.7764 (tt0) REVERT: o 1306 LYS cc_start: 0.6795 (mttt) cc_final: 0.6289 (mmmt) REVERT: o 1351 ASP cc_start: 0.8031 (m-30) cc_final: 0.7572 (m-30) REVERT: o 1423 ASP cc_start: 0.7602 (m-30) cc_final: 0.6713 (t0) REVERT: p 87 LYS cc_start: 0.6751 (tttt) cc_final: 0.6374 (tptt) REVERT: p 109 MET cc_start: 0.7003 (mmm) cc_final: 0.6696 (mmm) REVERT: p 233 SER cc_start: 0.6849 (t) cc_final: 0.6637 (p) REVERT: p 255 ARG cc_start: 0.6155 (mtm110) cc_final: 0.5647 (mtm-85) REVERT: p 335 ARG cc_start: 0.6082 (mtm-85) cc_final: 0.5164 (mtm-85) REVERT: p 381 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7625 (mp0) REVERT: p 386 ASP cc_start: 0.6667 (m-30) cc_final: 0.6089 (m-30) REVERT: p 388 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: p 414 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5092 (mp0) REVERT: p 442 ASP cc_start: 0.6322 (m-30) cc_final: 0.5999 (m-30) REVERT: p 528 LEU cc_start: 0.8287 (mt) cc_final: 0.8070 (mt) REVERT: p 551 GLU cc_start: 0.7274 (mp0) cc_final: 0.6907 (mp0) REVERT: p 597 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7911 (mp) REVERT: p 600 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6815 (pt0) REVERT: p 601 VAL cc_start: 0.8349 (t) cc_final: 0.7977 (t) REVERT: p 606 ASP cc_start: 0.6339 (t0) cc_final: 0.6036 (t0) REVERT: p 683 GLN cc_start: 0.7685 (mm110) cc_final: 0.7305 (mm-40) REVERT: p 747 LEU cc_start: 0.8023 (mt) cc_final: 0.7753 (mp) REVERT: p 952 GLU cc_start: 0.7421 (pt0) cc_final: 0.7153 (pm20) REVERT: p 958 CYS cc_start: 0.8397 (p) cc_final: 0.7964 (p) REVERT: p 1080 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7260 (mtp85) REVERT: p 1106 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6937 (tpm-80) REVERT: p 1121 LEU cc_start: 0.8162 (mt) cc_final: 0.7866 (mt) REVERT: p 1131 ARG cc_start: 0.8702 (mtt-85) cc_final: 0.8412 (mtp85) REVERT: p 1143 LYS cc_start: 0.6674 (OUTLIER) cc_final: 0.6436 (tttp) REVERT: q 17 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7394 (tt0) REVERT: q 44 ILE cc_start: 0.6486 (OUTLIER) cc_final: 0.6043 (pt) REVERT: q 83 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7508 (mt0) REVERT: q 126 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6789 (mmm-85) REVERT: q 185 GLU cc_start: 0.8239 (tt0) cc_final: 0.7672 (tt0) REVERT: s 61 LEU cc_start: 0.8843 (tp) cc_final: 0.8499 (tm) REVERT: s 210 GLN cc_start: 0.6382 (mt0) cc_final: 0.5870 (tm-30) REVERT: t 86 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7739 (mt-10) REVERT: t 112 ASP cc_start: 0.8301 (p0) cc_final: 0.8046 (p0) REVERT: t 114 SER cc_start: 0.7441 (t) cc_final: 0.6932 (p) REVERT: u 12 LEU cc_start: 0.9207 (mp) cc_final: 0.8825 (mm) REVERT: u 111 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.8101 (p-80) REVERT: u 117 MET cc_start: 0.2878 (mmp) cc_final: 0.1201 (mtm) REVERT: u 120 ASP cc_start: 0.4728 (m-30) cc_final: 0.3630 (p0) REVERT: u 164 MET cc_start: 0.5645 (mmt) cc_final: 0.5179 (mmt) REVERT: v 14 ASP cc_start: 0.6694 (m-30) cc_final: 0.6205 (t0) REVERT: v 23 ASP cc_start: 0.7735 (m-30) cc_final: 0.7408 (m-30) REVERT: v 63 THR cc_start: 0.8958 (p) cc_final: 0.8693 (t) REVERT: v 95 LYS cc_start: 0.6512 (tttt) cc_final: 0.6310 (ttmt) REVERT: v 100 GLU cc_start: 0.7444 (tt0) cc_final: 0.6795 (mt-10) REVERT: w 15 ARG cc_start: 0.7864 (ptp90) cc_final: 0.7273 (pmm-80) REVERT: w 40 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6704 (mmt180) REVERT: x 26 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: y 23 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7434 (tttm) REVERT: y 48 SER cc_start: 0.8058 (t) cc_final: 0.7780 (p) REVERT: y 70 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8018 (ttmm) REVERT: y 110 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7812 (ttmm) REVERT: z 15 MET cc_start: 0.5565 (mpt) cc_final: 0.5255 (mpt) REVERT: z 56 ASP cc_start: 0.6813 (m-30) cc_final: 0.6432 (p0) outliers start: 112 outliers final: 69 residues processed: 611 average time/residue: 1.5467 time to fit residues: 1135.9435 Evaluate side-chains 631 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 544 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 29 ASP Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 61 ARG Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 106 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 235 VAL Chi-restraints excluded: chain o residue 271 ARG Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 322 LEU Chi-restraints excluded: chain o residue 329 MET Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 508 SER Chi-restraints excluded: chain o residue 534 VAL Chi-restraints excluded: chain o residue 612 ASP Chi-restraints excluded: chain o residue 636 ILE Chi-restraints excluded: chain o residue 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 725 LEU Chi-restraints excluded: chain o residue 728 THR Chi-restraints excluded: chain o residue 787 VAL Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 947 HIS Chi-restraints excluded: chain o residue 1136 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1180 ASN Chi-restraints excluded: chain o residue 1234 LYS Chi-restraints excluded: chain o residue 1263 ASN Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1367 THR Chi-restraints excluded: chain o residue 1379 GLU Chi-restraints excluded: chain o residue 1398 LEU Chi-restraints excluded: chain o residue 1412 MET Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 56 GLN Chi-restraints excluded: chain p residue 173 GLU Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 297 MET Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 546 GLU Chi-restraints excluded: chain p residue 595 ASP Chi-restraints excluded: chain p residue 597 ILE Chi-restraints excluded: chain p residue 598 VAL Chi-restraints excluded: chain p residue 603 MET Chi-restraints excluded: chain p residue 650 ASN Chi-restraints excluded: chain p residue 677 MET Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1106 ARG Chi-restraints excluded: chain p residue 1125 MET Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain p residue 1143 LYS Chi-restraints excluded: chain p residue 1144 THR Chi-restraints excluded: chain p residue 1172 MET Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 83 GLN Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 86 THR Chi-restraints excluded: chain t residue 81 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain u residue 166 ASP Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 55 LYS Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 14 ILE Chi-restraints excluded: chain w residue 22 ASN Chi-restraints excluded: chain w residue 40 ARG Chi-restraints excluded: chain w residue 73 SER Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain x residue 26 GLN Chi-restraints excluded: chain x residue 53 VAL Chi-restraints excluded: chain y residue 20 THR Chi-restraints excluded: chain y residue 78 THR Chi-restraints excluded: chain z residue 52 LEU 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: 1.9990 chunk 102 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 92 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 343 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 136 GLN ** o 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 947 HIS p 23 GLN ** p 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 315 ASN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p1007 ASN ** s 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 168 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 76 ASN v 126 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118925 restraints weight = 46492.272| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.02 r_work: 0.3229 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36635 Z= 0.293 Angle : 0.498 9.686 49969 Z= 0.262 Chirality : 0.041 0.174 5568 Planarity : 0.004 0.061 6099 Dihedral : 16.163 120.525 5822 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 32.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.39 % Favored : 94.39 % Rotamer: Outliers : 2.93 % Allowed : 23.10 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 4137 helix: 1.92 (0.14), residues: 1393 sheet: 0.11 (0.20), residues: 671 loop : -0.29 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP o1192 HIS 0.010 0.001 HIS o 947 PHE 0.023 0.001 PHE o 397 TYR 0.017 0.002 TYR t 115 ARG 0.010 0.000 ARG u 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18549.55 seconds wall clock time: 326 minutes 23.74 seconds (19583.74 seconds total)