Starting phenix.real_space_refine on Sat Mar 23 05:47:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8waw_37407/03_2024/8waw_37407_trim_updated.pdb" } resolution = 3.02 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= 0.092 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 115 5.49 5 Mg 1 5.21 5 S 203 5.16 5 C 22167 2.51 5 N 6278 2.21 5 O 6966 1.98 5 H 23 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "o TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 788": "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" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35761 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: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1116 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "Z" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 281 Unusual residues: {'ATP': 1} Classifications: {'RNA': 12, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 10, None: 1} Not linked: pdbres="ATP Z 1 " pdbres=" U Z 2 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "o" Number of atoms: 11510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1452, 11510 Classifications: {'peptide': 1452} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1381} Chain breaks: 1 Chain: "p" Number of atoms: 9149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 9149 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 53, 'TRANS': 1092} Chain breaks: 1 Chain: "q" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "r" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "s" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "t" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "u" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "v" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "w" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "x" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "y" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "z" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "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 4749 SG CYS o 71 114.042 112.502 115.204 1.00141.57 S ATOM 4771 SG CYS o 74 111.778 115.426 115.261 1.00137.29 S ATOM 4818 SG CYS o 81 110.339 111.856 114.994 1.00138.71 S ATOM 5053 SG CYS o 111 101.613 111.261 68.339 1.00164.45 S ATOM 5081 SG CYS o 114 103.708 114.595 68.108 1.00163.67 S ATOM 5427 SG CYS o 184 103.780 111.936 65.273 1.00171.81 S ATOM 24514 SG CYS p1119 105.513 124.991 104.052 1.00141.59 S ATOM 24536 SG CYS p1122 105.489 121.802 101.888 1.00142.57 S ATOM 24651 SG CYS p1137 108.341 122.495 104.054 1.00148.67 S ATOM 24672 SG CYS p1140 107.841 124.313 100.786 1.00152.98 S ATOM 25638 SG CYS q 88 85.556 90.757 173.435 1.00138.12 S ATOM 25651 SG CYS q 90 89.018 89.794 172.366 1.00147.15 S ATOM 25686 SG CYS q 94 87.151 87.436 174.646 1.00132.97 S ATOM 25708 SG CYS q 97 85.771 87.769 171.241 1.00132.45 S ATOM 33014 SG CYS w 17 75.596 52.432 55.883 1.00161.53 S ATOM 33038 SG CYS w 20 78.996 53.547 57.324 1.00163.91 S ATOM 33199 SG CYS w 39 76.776 56.223 56.456 1.00169.29 S ATOM 33224 SG CYS w 42 78.039 54.022 53.633 1.00167.79 S ATOM 33576 SG CYS w 86 44.276 43.117 86.134 1.00150.39 S ATOM 33600 SG CYS w 89 44.891 39.680 87.853 1.00155.57 S ATOM 33804 SG CYS w 114 46.560 42.872 89.164 1.00146.35 S ATOM 33839 SG CYS w 119 47.419 41.333 85.709 1.00152.45 S ATOM 33949 SG CYS x 7 65.613 72.270 151.585 1.00 98.61 S ATOM 33973 SG CYS x 10 63.956 73.320 154.832 1.00 95.35 S ATOM 34237 SG CYS x 44 61.794 72.488 151.627 1.00107.46 S ATOM 34243 SG CYS x 45 63.266 70.101 154.093 1.00108.23 S ATOM 35389 SG CYS z 19 107.118 61.295 142.338 1.00146.64 S ATOM 35408 SG CYS z 22 108.002 58.760 144.907 1.00145.85 S ATOM 35525 SG CYS z 36 110.712 61.364 143.988 1.00153.01 S ATOM 35551 SG CYS z 39 109.498 58.961 141.330 1.00150.68 S Time building chain proxies: 18.07, per 1000 atoms: 0.51 Number of scatterers: 35761 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 115 15.00 Mg 1 11.99 O 6966 8.00 N 6278 7.00 C 22167 6.00 H 23 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.69 Conformation dependent library (CDL) restraints added in 5.5 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 39 " pdb="ZN ZN w 201 " - pdb=" SG CYS w 17 " pdb=" ZN w 202 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 119 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 86 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 89 " pdb="ZN ZN w 202 " - pdb=" SG CYS w 114 " pdb=" ZN x 101 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 10 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 45 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 44 " pdb="ZN ZN x 101 " - pdb=" SG CYS x 7 " pdb=" ZN z 101 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 39 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 19 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 22 " pdb="ZN ZN z 101 " - pdb=" SG CYS z 36 " Number of angles added : 39 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 43 sheets defined 32.5% alpha, 14.8% beta 42 base pairs and 91 stacking pairs defined. Time for finding SS restraints: 15.26 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: 4.168A 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: 4.257A pdb=" N GLY o 150 " --> pdb=" O ASP o 146 " (cutoff:3.500A) Processing helix chain 'o' and resid 218 through 227 removed outlier: 3.838A 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: 4.222A pdb=" N THR o 490 " --> pdb=" O SER o 487 " (cutoff:3.500A) Proline residue: o 491 - end of helix Processing helix chain 'o' and resid 509 through 519 Processing helix chain 'o' and resid 521 through 524 Processing helix chain 'o' and resid 539 through 548 removed outlier: 3.584A pdb=" N LYS o 547 " --> pdb=" O ALA o 544 " (cutoff:3.500A) Processing helix chain 'o' and resid 557 through 566 removed outlier: 3.829A pdb=" N PHE o 566 " --> pdb=" O ASN o 562 " (cutoff:3.500A) Processing helix chain 'o' and resid 588 through 595 removed outlier: 3.883A pdb=" N LEU o 594 " --> pdb=" O GLN o 590 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE o 595 " --> pdb=" O ILE o 591 " (cutoff:3.500A) Processing helix chain 'o' and resid 611 through 615 removed outlier: 4.212A 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: 4.425A pdb=" N ALA o 855 " --> pdb=" O ALA o 851 " (cutoff:3.500A) removed outlier: 3.828A 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 1019 Processing helix chain 'o' and resid 1028 through 1037 Processing helix chain 'o' and resid 1039 through 1048 Processing helix chain 'o' and resid 1051 through 1056 Processing helix chain 'o' and resid 1062 through 1079 Processing helix chain 'o' and resid 1087 through 1101 Proline residue: o1098 - end of helix removed outlier: 4.100A 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: 3.756A pdb=" N GLU o1191 " --> pdb=" O GLU o1188 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL o1193 " --> pdb=" O GLN o1190 " (cutoff:3.500A) Processing helix chain 'o' and resid 1218 through 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: 3.799A 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: 3.813A 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: 3.771A 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: 3.502A pdb=" N THR p 723 " --> pdb=" O SER p 719 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN p 731 " --> pdb=" O ALA p 727 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 741 removed outlier: 4.627A 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: 3.527A pdb=" N ASP p1017 " --> pdb=" O ASN p1013 " (cutoff:3.500A) removed outlier: 3.826A 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: 4.044A pdb=" N ALA p1110 " --> pdb=" O ARG p1106 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.589A pdb=" N VAL q 245 " --> pdb=" O PRO q 241 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 27 No H-bonds generated for 'chain 'r' and resid 24 through 27' Processing helix chain 'r' and resid 34 through 50 Processing helix chain 'r' and resid 59 through 70 Processing helix chain 'r' and resid 77 through 89 Processing helix chain 'r' and resid 94 through 103 Processing helix chain 'r' and resid 108 through 114 Processing helix chain 'r' and resid 116 through 118 No H-bonds generated for 'chain 'r' and resid 116 through 118' Processing helix chain 'r' and resid 124 through 137 Processing helix chain 's' and resid 3 through 23 Processing helix chain 's' and resid 30 through 33 No H-bonds generated for 'chain 's' and resid 30 through 33' Processing helix chain 's' and resid 37 through 44 Processing helix chain 's' and resid 84 through 97 Processing helix chain 's' and resid 112 through 120 Processing helix chain 's' and resid 134 through 136 No H-bonds generated for 'chain 's' and resid 134 through 136' Processing helix chain 's' and resid 139 through 141 No H-bonds generated for 'chain 's' and resid 139 through 141' Processing helix chain 's' and resid 153 through 162 Processing helix chain 's' and resid 178 through 183 Processing helix chain 't' and resid 59 through 75 Processing helix chain 't' and resid 89 through 99 Processing helix chain 'u' and resid 15 through 17 No H-bonds generated for 'chain 'u' and resid 15 through 17' Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'w' and resid 64 through 66 No H-bonds generated for 'chain 'w' and resid 64 through 66' Processing helix chain 'w' and resid 70 through 74 Processing helix chain 'x' and resid 15 through 27 removed outlier: 4.109A pdb=" N TRP x 18 " --> pdb=" O GLY x 15 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLU x 19 " --> pdb=" O ASN x 16 " (cutoff:3.500A) removed outlier: 3.580A 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: 3.578A pdb=" N MET x 48 " --> pdb=" O CYS x 44 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU x 49 " --> pdb=" O CYS x 45 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 61 removed outlier: 3.596A 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: 3.852A pdb=" N ILE y 45 " --> pdb=" O THR y 41 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 112 Processing sheet with id= A, first strand: chain 'S' and resid 27 through 31 removed outlier: 6.826A pdb=" N ASN S 142 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA S 30 " --> pdb=" O ASN S 142 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR S 144 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE S 113 " --> pdb=" O ASN S 145 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS S 109 " --> pdb=" O LEU S 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 125 through 128 removed outlier: 3.581A pdb=" N ILE S 126 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE S 138 " --> pdb=" O ILE S 126 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR S 128 " --> pdb=" O GLU S 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU S 136 " --> pdb=" O THR S 128 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'T' and resid 41 through 47 removed outlier: 11.280A 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: 3.914A pdb=" N ARG T 113 " --> pdb=" O GLN T 86 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU T 20 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG T 113 " --> pdb=" O LEU T 20 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS T 22 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 4.688A 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: 3.604A pdb=" N GLY T 108 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 6.529A 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: 4.627A 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: 3.546A 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: 6.115A 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: 3.962A pdb=" N TYR o 418 " --> pdb=" O GLU o 447 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS o 449 " --> pdb=" O ALA o 416 " (cutoff:3.500A) removed outlier: 7.142A 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: 3.575A pdb=" N MET o 637 " --> pdb=" O VAL o 629 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU o 631 " --> pdb=" O LEU o 635 " (cutoff:3.500A) removed outlier: 5.114A 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: 3.677A pdb=" N LYS o1306 " --> pdb=" O ASP o1339 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'o' and resid 1244 through 1247 removed outlier: 4.361A pdb=" N LEU o1255 " --> pdb=" O LEU o1216 " (cutoff:3.500A) removed outlier: 3.605A 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: 3.724A pdb=" N GLY p 150 " --> pdb=" O LEU p 124 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL p 126 " --> pdb=" O PHE p 148 " (cutoff:3.500A) removed outlier: 5.223A 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: 6.875A pdb=" N MET p 239 " --> pdb=" O ALA p 216 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR p 218 " --> pdb=" O VAL p 237 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL p 237 " --> pdb=" O THR p 218 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU p 220 " --> pdb=" O ILE p 235 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE p 235 " --> pdb=" O GLU p 220 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ARG p 222 " --> pdb=" O SER p 233 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER p 233 " --> pdb=" O ARG p 222 " (cutoff:3.500A) removed outlier: 3.613A 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: 3.558A pdb=" N GLN p 906 " --> pdb=" O ARG p 922 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG p 924 " --> pdb=" O VAL p 904 " (cutoff:3.500A) removed outlier: 5.422A 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: 6.881A pdb=" N VAL p 794 " --> pdb=" O GLY p 946 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN p 948 " --> pdb=" O VAL p 794 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET p 796 " --> pdb=" O GLN p 948 " (cutoff:3.500A) removed outlier: 4.352A 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: 6.826A pdb=" N ILE q 22 " --> pdb=" O ILE q 11 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE q 11 " --> pdb=" O ILE q 22 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLU q 24 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL q 9 " --> pdb=" O GLU q 24 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 98 through 106 removed outlier: 6.058A pdb=" N LYS q 166 " --> pdb=" O ILE q 47 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE q 47 " --> pdb=" O LYS q 166 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY q 168 " --> pdb=" O ILE q 45 " (cutoff:3.500A) removed outlier: 5.013A 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: 6.284A pdb=" N ILE s 126 " --> pdb=" O ALA s 102 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE s 104 " --> pdb=" O ILE s 126 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU s 128 " --> pdb=" O ILE s 104 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL s 106 " --> pdb=" O GLU s 128 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE s 130 " --> pdb=" O VAL s 106 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 's' and resid 147 through 150 removed outlier: 3.678A 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: 3.557A pdb=" N ALA u 47 " --> pdb=" O ILE u 75 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE u 77 " --> pdb=" O VAL u 45 " (cutoff:3.500A) removed outlier: 5.664A 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: 7.007A pdb=" N PHE u 98 " --> pdb=" O THR u 90 " (cutoff:3.500A) removed outlier: 5.494A 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: 4.267A 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: 3.761A pdb=" N GLY u 149 " --> pdb=" O ILE u 160 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER u 162 " --> pdb=" O ILE u 147 " (cutoff:3.500A) removed outlier: 5.914A 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: 6.851A 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: 5.335A pdb=" N LEU v 122 " --> pdb=" O ASP v 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER v 117 " --> pdb=" O VAL v 96 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL v 96 " --> pdb=" O SER v 117 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS v 55 " --> pdb=" O LEU v 148 " (cutoff:3.500A) removed outlier: 6.720A 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 1148 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 91 stacking parallelities Total time for adding SS restraints: 18.89 Time building geometry restraints manager: 14.75 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: 9184 1.33 - 1.49: 12035 1.49 - 1.65: 15097 1.65 - 1.81: 325 Bond restraints: 36664 Sorted by residual: bond pdb=" C2' G2L Z 13 " pdb=" C1' G2L Z 13 " 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 13 " pdb=" C3' G2L Z 13 " ideal model delta sigma weight residual 1.270 1.520 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" ND2 ASN N 7 " pdb="HD22 ASN N 7 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N ILE N 4 " pdb=" H ILE N 4 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N GLY N 3 " pdb=" H GLY N 3 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 36659 not shown) Histogram of bond angle deviations from ideal: 75.33 - 88.70: 1 88.70 - 102.08: 263 102.08 - 115.45: 24234 115.45 - 128.83: 25241 128.83 - 142.20: 292 Bond angle restraints: 50031 Sorted by residual: angle pdb=" N09 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" O05 W0F p1201 " ideal model delta sigma weight residual 110.18 75.33 34.85 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C07 W0F p1201 " pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " ideal model delta sigma weight residual 110.46 136.31 -25.85 3.00e+00 1.11e-01 7.42e+01 angle pdb=" P26 W0F p1201 " pdb=" O29 W0F p1201 " pdb=" P30 W0F p1201 " ideal model delta sigma weight residual 123.60 142.20 -18.60 3.00e+00 1.11e-01 3.85e+01 angle pdb=" C06 W0F p1201 " pdb=" N09 W0F p1201 " pdb=" C10 W0F p1201 " ideal model delta sigma weight residual 99.38 117.55 -18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" C ASP p 355 " pdb=" CA ASP p 355 " pdb=" CB ASP p 355 " ideal model delta sigma weight residual 116.63 110.19 6.44 1.16e+00 7.43e-01 3.08e+01 ... (remaining 50026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.18: 21109 30.18 - 60.37: 1008 60.37 - 90.55: 40 90.55 - 120.74: 2 120.74 - 150.92: 3 Dihedral angle restraints: 22162 sinusoidal: 10002 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 200.00 49.08 150.92 1 1.50e+01 4.44e-03 8.00e+01 dihedral pdb=" CA TRP o 479 " pdb=" C TRP o 479 " pdb=" N SER o 480 " pdb=" CA SER o 480 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PRO w 117 " pdb=" C PRO w 117 " pdb=" N HIS w 118 " pdb=" CA HIS w 118 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 22159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4955 0.075 - 0.149: 596 0.149 - 0.224: 12 0.224 - 0.298: 1 0.298 - 0.373: 3 Chirality restraints: 5567 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 3.47e+00 chirality pdb=" CA HYP N 8 " pdb=" N HYP N 8 " pdb=" C HYP N 8 " pdb=" CB HYP N 8 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C03 W0F p1201 " pdb=" C04 W0F p1201 " pdb=" C07 W0F p1201 " pdb=" O02 W0F p1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 5564 not shown) Planarity restraints: 6103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 W0F p1201 " -0.108 2.00e-02 2.50e+03 4.14e-02 5.15e+01 pdb=" C10 W0F p1201 " 0.040 2.00e-02 2.50e+03 pdb=" C12 W0F p1201 " 0.007 2.00e-02 2.50e+03 pdb=" C13 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" C15 W0F p1201 " 0.007 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 " 0.013 2.00e-02 2.50e+03 pdb=" N14 W0F p1201 " 0.031 2.00e-02 2.50e+03 pdb=" N16 W0F p1201 " -0.018 2.00e-02 2.50e+03 pdb=" N19 W0F p1201 " 0.006 2.00e-02 2.50e+03 pdb=" O18 W0F p1201 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE p 51 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C ILE p 51 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE p 51 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN p 52 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE p 50 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PHE p 50 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE p 50 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE p 51 " -0.024 2.00e-02 2.50e+03 ... (remaining 6100 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.38: 47 2.38 - 2.94: 15518 2.94 - 3.49: 41428 3.49 - 4.05: 71008 4.05 - 4.60: 102044 Nonbonded interactions: 230045 Sorted by model distance: nonbonded pdb=" OD1 ASP o 495 " pdb="MG MG o2003 " model vdw 1.829 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 1.950 2.050 nonbonded pdb=" OD2 ASP o 497 " pdb=" O33 W0F p1201 " model vdw 2.019 2.800 nonbonded pdb="HG22 ILE N 4 " pdb="HD13 ILE N 4 " model vdw 2.021 2.440 ... (remaining 230040 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: 1.480 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: 0.820 Extract box with map and model: 8.450 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 107.340 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 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 : 0.005 0.251 36641 Z= 0.328 Angle : 0.712 34.850 49979 Z= 0.368 Chirality : 0.045 0.373 5567 Planarity : 0.004 0.059 6099 Dihedral : 15.439 150.922 14289 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 1.25 % Allowed : 6.16 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 4137 helix: 1.34 (0.14), residues: 1416 sheet: 0.18 (0.20), residues: 656 loop : -0.26 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP o1192 HIS 0.006 0.001 HIS o 809 PHE 0.019 0.002 PHE q 93 TYR 0.025 0.002 TYR o 669 ARG 0.004 0.000 ARG v 27 *********************** 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 1042 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 996 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 18 ILE cc_start: 0.8214 (mt) cc_final: 0.7764 (mm) REVERT: o 31 LEU cc_start: 0.7496 (mt) cc_final: 0.7170 (mt) REVERT: o 67 ARG cc_start: 0.8953 (ttp80) cc_final: 0.8411 (ttm110) REVERT: o 184 CYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7204 (p) REVERT: o 187 TYR cc_start: 0.8006 (m-80) cc_final: 0.7704 (m-10) REVERT: o 192 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7698 (ptm-80) REVERT: o 193 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7669 (tmm-80) REVERT: o 201 GLU cc_start: 0.7529 (tt0) cc_final: 0.7265 (pt0) REVERT: o 437 ASP cc_start: 0.7562 (m-30) cc_final: 0.7148 (m-30) REVERT: o 451 CYS cc_start: 0.6661 (m) cc_final: 0.6312 (p) REVERT: o 484 LEU cc_start: 0.8483 (pp) cc_final: 0.8267 (pp) REVERT: o 520 MET cc_start: 0.7748 (tpt) cc_final: 0.7501 (tpp) REVERT: o 532 ARG cc_start: 0.6794 (mtm110) cc_final: 0.6066 (ptp90) REVERT: o 556 GLU cc_start: 0.6876 (pt0) cc_final: 0.6674 (mt-10) REVERT: o 561 MET cc_start: 0.7654 (mtt) cc_final: 0.7399 (mtt) REVERT: o 700 GLN cc_start: 0.7352 (tt0) cc_final: 0.7075 (tp-100) REVERT: o 766 PHE cc_start: 0.7835 (m-80) cc_final: 0.7620 (m-80) REVERT: o 803 LYS cc_start: 0.7656 (tttp) cc_final: 0.7327 (ttpt) REVERT: o 824 GLU cc_start: 0.7352 (pt0) cc_final: 0.6885 (mp0) REVERT: o 868 MET cc_start: 0.8021 (ptt) cc_final: 0.7722 (ptm) REVERT: o 1034 GLN cc_start: 0.6941 (tt0) cc_final: 0.6525 (tp40) REVERT: o 1128 ILE cc_start: 0.6964 (mm) cc_final: 0.6443 (tt) REVERT: o 1132 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8249 (mmtm) REVERT: o 1212 LEU cc_start: 0.7767 (tp) cc_final: 0.7283 (tt) REVERT: o 1220 HIS cc_start: 0.7212 (m-70) cc_final: 0.6904 (m-70) REVERT: o 1221 MET cc_start: 0.8366 (mmm) cc_final: 0.8016 (mmm) REVERT: o 1259 ILE cc_start: 0.8327 (mt) cc_final: 0.8003 (mp) REVERT: o 1284 PHE cc_start: 0.8190 (t80) cc_final: 0.7861 (t80) REVERT: o 1306 LYS cc_start: 0.7215 (mttt) cc_final: 0.6857 (mttm) REVERT: o 1337 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6670 (pt0) REVERT: o 1344 MET cc_start: 0.6642 (tpp) cc_final: 0.6280 (tpt) REVERT: o 1351 ASP cc_start: 0.7955 (m-30) cc_final: 0.7491 (t0) REVERT: o 1372 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7405 (mm-30) REVERT: o 1383 TYR cc_start: 0.7374 (t80) cc_final: 0.7167 (t80) REVERT: o 1389 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: o 1391 SER cc_start: 0.7806 (t) cc_final: 0.7378 (p) REVERT: o 1396 ARG cc_start: 0.7076 (mtt-85) cc_final: 0.6842 (mtp85) REVERT: o 1412 MET cc_start: 0.7394 (ttp) cc_final: 0.6748 (ttp) REVERT: o 1414 ILE cc_start: 0.8105 (mm) cc_final: 0.7401 (mp) REVERT: o 1422 GLN cc_start: 0.7296 (mt0) cc_final: 0.6124 (mm110) REVERT: o 1423 ASP cc_start: 0.7554 (m-30) cc_final: 0.6774 (t0) REVERT: o 1472 ASP cc_start: 0.7572 (t0) cc_final: 0.7265 (t0) REVERT: o 1479 LYS cc_start: 0.6521 (ttmm) cc_final: 0.6258 (tptp) REVERT: p 17 ILE cc_start: 0.8595 (mt) cc_final: 0.8390 (mm) REVERT: p 46 SER cc_start: 0.6455 (t) cc_final: 0.6203 (m) REVERT: p 109 MET cc_start: 0.7992 (mmm) cc_final: 0.7505 (mmt) REVERT: p 111 ASN cc_start: 0.6752 (t0) cc_final: 0.6544 (t0) REVERT: p 141 GLN cc_start: 0.8782 (pt0) cc_final: 0.8112 (pp30) REVERT: p 168 ASP cc_start: 0.7180 (p0) cc_final: 0.6656 (m-30) REVERT: p 215 TYR cc_start: 0.7806 (m-80) cc_final: 0.7342 (m-80) REVERT: p 239 MET cc_start: 0.7584 (ttm) cc_final: 0.7234 (ttp) REVERT: p 313 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7236 (mt-10) REVERT: p 324 ARG cc_start: 0.8314 (mtt90) cc_final: 0.6711 (mtp85) REVERT: p 346 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6377 (mt-10) REVERT: p 377 LEU cc_start: 0.7421 (mt) cc_final: 0.7043 (mt) REVERT: p 381 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8352 (mp0) REVERT: p 416 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6828 (ttm-80) REVERT: p 543 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6574 (mt-10) REVERT: p 563 ASP cc_start: 0.4037 (m-30) cc_final: 0.3746 (m-30) REVERT: p 576 ILE cc_start: 0.7969 (pt) cc_final: 0.7672 (pt) REVERT: p 606 ASP cc_start: 0.6432 (t0) cc_final: 0.4964 (t0) REVERT: p 608 ARG cc_start: 0.6306 (ttp80) cc_final: 0.5096 (ttm-80) REVERT: p 648 TYR cc_start: 0.7822 (p90) cc_final: 0.7516 (p90) REVERT: p 649 ASN cc_start: 0.7697 (t0) cc_final: 0.7410 (t0) REVERT: p 670 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: p 677 MET cc_start: 0.7811 (mmm) cc_final: 0.6753 (tpp) REVERT: p 697 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7950 (mt-10) REVERT: p 728 MET cc_start: 0.7161 (mtm) cc_final: 0.6921 (mtp) REVERT: p 747 LEU cc_start: 0.8267 (mt) cc_final: 0.8040 (mp) REVERT: p 768 ARG cc_start: 0.7628 (mmt180) cc_final: 0.7376 (mmm-85) REVERT: p 792 ASP cc_start: 0.6955 (m-30) cc_final: 0.6731 (m-30) REVERT: p 817 GLN cc_start: 0.7104 (tt0) cc_final: 0.6557 (pm20) REVERT: p 832 PRO cc_start: 0.8692 (Cg_exo) cc_final: 0.8049 (Cg_endo) REVERT: p 863 ASP cc_start: 0.7485 (m-30) cc_final: 0.6789 (t0) REVERT: p 906 GLN cc_start: 0.7396 (tt0) cc_final: 0.7089 (tt0) REVERT: p 995 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7218 (pt0) REVERT: p 1007 ASN cc_start: 0.7862 (m-40) cc_final: 0.7642 (m-40) REVERT: p 1076 GLU cc_start: 0.7820 (tt0) cc_final: 0.7363 (tt0) REVERT: p 1080 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7364 (mtp85) REVERT: p 1093 CYS cc_start: 0.5856 (m) cc_final: 0.5594 (m) REVERT: p 1114 TYR cc_start: 0.7227 (t80) cc_final: 0.6960 (t80) REVERT: p 1121 LEU cc_start: 0.8148 (mt) cc_final: 0.7750 (mt) REVERT: p 1151 MET cc_start: 0.7775 (ptm) cc_final: 0.7414 (ptp) REVERT: p 1172 MET cc_start: 0.7106 (mmt) cc_final: 0.6119 (mmm) REVERT: q 83 GLN cc_start: 0.8317 (mt0) cc_final: 0.8082 (mt0) REVERT: q 199 LYS cc_start: 0.8364 (mttt) cc_final: 0.8089 (mtmm) REVERT: r 38 HIS cc_start: 0.8272 (t70) cc_final: 0.8024 (t70) REVERT: s 91 CYS cc_start: 0.8599 (t) cc_final: 0.8359 (t) REVERT: s 117 SER cc_start: 0.8249 (m) cc_final: 0.7966 (t) REVERT: s 120 ASP cc_start: 0.8391 (m-30) cc_final: 0.7065 (m-30) REVERT: s 133 GLN cc_start: 0.7487 (mt0) cc_final: 0.6576 (mm-40) REVERT: s 172 ARG cc_start: 0.7172 (mtt180) cc_final: 0.6705 (mtt-85) REVERT: s 177 ASP cc_start: 0.7496 (t70) cc_final: 0.7159 (t70) REVERT: t 53 THR cc_start: 0.8067 (p) cc_final: 0.7850 (p) REVERT: t 57 MET cc_start: 0.7170 (ttp) cc_final: 0.6918 (ttm) REVERT: t 59 LYS cc_start: 0.6507 (ptpt) cc_final: 0.6254 (ptpp) REVERT: t 76 CYS cc_start: 0.7594 (t) cc_final: 0.7327 (m) REVERT: t 79 VAL cc_start: 0.7750 (t) cc_final: 0.7407 (p) REVERT: t 80 MET cc_start: 0.7799 (mmt) cc_final: 0.7246 (mmt) REVERT: t 86 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6895 (mp0) REVERT: t 115 TYR cc_start: 0.8020 (p90) cc_final: 0.7784 (p90) REVERT: u 69 PRO cc_start: 0.6817 (Cg_exo) cc_final: 0.6611 (Cg_endo) REVERT: u 104 MET cc_start: 0.8933 (ttp) cc_final: 0.8194 (ppp) REVERT: u 157 ILE cc_start: 0.7569 (mt) cc_final: 0.7044 (mt) REVERT: v 9 ILE cc_start: 0.8171 (mp) cc_final: 0.7614 (mt) REVERT: v 35 PHE cc_start: 0.7512 (m-80) cc_final: 0.7170 (m-10) REVERT: v 37 MET cc_start: 0.7751 (mtp) cc_final: 0.7282 (mtp) REVERT: v 63 THR cc_start: 0.9295 (p) cc_final: 0.8989 (t) REVERT: v 76 ASN cc_start: 0.8455 (m-40) cc_final: 0.8092 (t0) REVERT: v 98 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6677 (mtp85) REVERT: v 100 GLU cc_start: 0.7720 (tt0) cc_final: 0.6889 (pt0) REVERT: v 105 SER cc_start: 0.8887 (t) cc_final: 0.8591 (t) REVERT: v 132 LEU cc_start: 0.8296 (mt) cc_final: 0.8074 (mt) REVERT: v 136 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7847 (mt-10) REVERT: v 146 LYS cc_start: 0.7467 (tttt) cc_final: 0.7065 (ttpp) REVERT: w 23 MET cc_start: 0.8084 (ttm) cc_final: 0.7694 (ttp) REVERT: w 50 ASN cc_start: 0.7545 (t0) cc_final: 0.7234 (t0) REVERT: w 54 TYR cc_start: 0.7246 (t80) cc_final: 0.6835 (t80) REVERT: w 68 ILE cc_start: 0.6869 (mm) cc_final: 0.6531 (mm) REVERT: w 69 ILE cc_start: 0.7870 (mt) cc_final: 0.7461 (mm) REVERT: w 71 ASP cc_start: 0.8247 (m-30) cc_final: 0.7887 (m-30) REVERT: w 93 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7659 (mt-10) REVERT: w 115 THR cc_start: 0.8709 (m) cc_final: 0.8274 (p) REVERT: x 47 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7525 (ttp-170) REVERT: x 58 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7612 (mmmm) REVERT: x 62 TYR cc_start: 0.7711 (m-80) cc_final: 0.7148 (m-80) REVERT: y 8 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7460 (mm-30) REVERT: y 24 ASP cc_start: 0.7635 (t70) cc_final: 0.7317 (t0) REVERT: y 27 VAL cc_start: 0.8404 (t) cc_final: 0.8098 (m) REVERT: y 48 SER cc_start: 0.8388 (t) cc_final: 0.8131 (m) REVERT: z 35 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7318 (ttm110) REVERT: z 46 LYS cc_start: 0.7002 (tptp) cc_final: 0.6766 (tptt) REVERT: z 50 LYS cc_start: 0.8655 (mttt) cc_final: 0.8335 (mptt) outliers start: 46 outliers final: 7 residues processed: 1023 average time/residue: 0.5581 time to fit residues: 865.3637 Evaluate side-chains 613 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 603 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 670 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain y residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 2.9990 chunk 319 optimal weight: 0.6980 chunk 177 optimal weight: 0.0040 chunk 109 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 329 optimal weight: 30.0000 chunk 127 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 245 optimal weight: 2.9990 chunk 382 optimal weight: 4.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** o 181 HIS o 278 HIS ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 301 HIS o 439 HIS ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN o 531 ASN o 539 GLN ** o 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 780 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 792 ASN o 804 HIS o1082 HIS ** o1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1422 GLN o1462 GLN p 43 GLN p 245 GLN p 319 ASN ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 525 ASN p 639 HIS p 699 HIS ** p 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 718 GLN p 838 GLN p 941 GLN p1021 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 262 GLN r 66 ASN r 129 GLN s 64 HIS ** s 98 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 24 ASN v 46 GLN v 126 GLN w 41 ASN w 45 GLN ** w 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 100 HIS y 84 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5641 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36641 Z= 0.229 Angle : 0.507 9.265 49979 Z= 0.272 Chirality : 0.041 0.202 5567 Planarity : 0.003 0.041 6099 Dihedral : 16.829 146.956 5850 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.06 % Rotamer: Outliers : 2.55 % Allowed : 11.82 % Favored : 85.63 % Cbeta Deviations : 0.03 % 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: 1.72 (0.14), residues: 1414 sheet: 0.08 (0.19), residues: 687 loop : -0.16 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP o1192 HIS 0.008 0.001 HIS o 804 PHE 0.028 0.002 PHE o 431 TYR 0.015 0.001 TYR o 669 ARG 0.013 0.000 ARG u 63 *********************** 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 724 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 630 time to evaluate : 4.113 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 29 ASP cc_start: 0.7687 (t0) cc_final: 0.7462 (t0) REVERT: o 31 LEU cc_start: 0.7279 (mt) cc_final: 0.6981 (mt) REVERT: o 67 ARG cc_start: 0.8741 (ttp80) cc_final: 0.8431 (ttm110) REVERT: o 192 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7805 (ptm-80) REVERT: o 193 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7887 (tmm-80) REVERT: o 201 GLU cc_start: 0.7527 (tt0) cc_final: 0.7262 (pt0) REVERT: o 321 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6808 (mp0) REVERT: o 437 ASP cc_start: 0.7398 (m-30) cc_final: 0.7191 (m-30) REVERT: o 451 CYS cc_start: 0.6774 (m) cc_final: 0.6387 (p) REVERT: o 532 ARG cc_start: 0.6894 (mtm110) cc_final: 0.6543 (ptm-80) REVERT: o 561 MET cc_start: 0.7385 (mtt) cc_final: 0.7051 (mtt) REVERT: o 700 GLN cc_start: 0.7374 (tt0) cc_final: 0.6736 (tp-100) REVERT: o 712 ASP cc_start: 0.7240 (m-30) cc_final: 0.6898 (m-30) REVERT: o 803 LYS cc_start: 0.7697 (tttp) cc_final: 0.7256 (ttpt) REVERT: o 824 GLU cc_start: 0.7506 (pt0) cc_final: 0.7028 (mp0) REVERT: o 868 MET cc_start: 0.8065 (ptt) cc_final: 0.7686 (ptm) REVERT: o 953 GLU cc_start: 0.7661 (tp30) cc_final: 0.7355 (tp30) REVERT: o 1034 GLN cc_start: 0.6877 (tt0) cc_final: 0.6627 (tm-30) REVERT: o 1128 ILE cc_start: 0.6850 (mm) cc_final: 0.6329 (tt) REVERT: o 1132 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8251 (mmtm) REVERT: o 1146 GLN cc_start: 0.8154 (pt0) cc_final: 0.7650 (pp30) REVERT: o 1212 LEU cc_start: 0.7693 (tp) cc_final: 0.7272 (tt) REVERT: o 1259 ILE cc_start: 0.8184 (mt) cc_final: 0.7947 (mp) REVERT: o 1306 LYS cc_start: 0.7162 (mttt) cc_final: 0.6870 (mttm) REVERT: o 1327 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6780 (tp30) REVERT: o 1337 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6538 (mt-10) REVERT: o 1344 MET cc_start: 0.6139 (tpp) cc_final: 0.5649 (tpt) REVERT: o 1351 ASP cc_start: 0.8087 (m-30) cc_final: 0.7808 (m-30) REVERT: o 1364 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6528 (mm-30) REVERT: o 1383 TYR cc_start: 0.7423 (t80) cc_final: 0.7160 (t80) REVERT: o 1391 SER cc_start: 0.8005 (t) cc_final: 0.7476 (p) REVERT: o 1422 GLN cc_start: 0.7194 (mt0) cc_final: 0.6158 (mm110) REVERT: o 1423 ASP cc_start: 0.7533 (m-30) cc_final: 0.6766 (t0) REVERT: o 1472 ASP cc_start: 0.7732 (t0) cc_final: 0.7522 (t0) REVERT: o 1478 GLU cc_start: 0.6884 (tt0) cc_final: 0.6290 (tp30) REVERT: o 1484 MET cc_start: 0.4424 (tmm) cc_final: 0.2759 (ppp) REVERT: p 36 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: p 46 SER cc_start: 0.7382 (t) cc_final: 0.7066 (m) REVERT: p 141 GLN cc_start: 0.8635 (pt0) cc_final: 0.8354 (pm20) REVERT: p 144 HIS cc_start: 0.7936 (m-70) cc_final: 0.7585 (m170) REVERT: p 168 ASP cc_start: 0.7127 (p0) cc_final: 0.6618 (m-30) REVERT: p 169 ARG cc_start: 0.7652 (tmm-80) cc_final: 0.7418 (tmm-80) REVERT: p 238 SER cc_start: 0.7439 (m) cc_final: 0.7004 (p) REVERT: p 309 PHE cc_start: 0.8562 (t80) cc_final: 0.8134 (t80) REVERT: p 324 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7597 (mmm-85) REVERT: p 344 GLN cc_start: 0.7674 (mt0) cc_final: 0.7283 (tt0) REVERT: p 346 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6382 (mt-10) REVERT: p 580 PRO cc_start: 0.7978 (Cg_endo) cc_final: 0.7723 (Cg_exo) REVERT: p 606 ASP cc_start: 0.6636 (t0) cc_final: 0.6314 (t0) REVERT: p 608 ARG cc_start: 0.6053 (ttp80) cc_final: 0.5829 (ttm-80) REVERT: p 677 MET cc_start: 0.8612 (mmm) cc_final: 0.8024 (tpp) REVERT: p 733 MET cc_start: 0.8457 (mtt) cc_final: 0.8129 (mtm) REVERT: p 747 LEU cc_start: 0.8483 (mt) cc_final: 0.8230 (mt) REVERT: p 792 ASP cc_start: 0.6849 (m-30) cc_final: 0.6590 (m-30) REVERT: p 815 LYS cc_start: 0.8490 (ptmm) cc_final: 0.8113 (ptmm) REVERT: p 817 GLN cc_start: 0.7053 (tt0) cc_final: 0.6518 (pm20) REVERT: p 841 ARG cc_start: 0.5375 (OUTLIER) cc_final: 0.5147 (mtm180) REVERT: p 863 ASP cc_start: 0.7601 (m-30) cc_final: 0.6767 (t0) REVERT: p 995 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7262 (pt0) REVERT: p 1007 ASN cc_start: 0.7793 (m-40) cc_final: 0.7475 (m-40) REVERT: p 1022 LEU cc_start: 0.7470 (mt) cc_final: 0.7157 (tp) REVERT: p 1080 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7338 (mtp85) REVERT: p 1114 TYR cc_start: 0.7325 (t80) cc_final: 0.7022 (t80) REVERT: p 1121 LEU cc_start: 0.8155 (mt) cc_final: 0.7796 (mt) REVERT: p 1141 ARG cc_start: 0.7061 (mmp80) cc_final: 0.6764 (mmp80) REVERT: p 1163 MET cc_start: 0.6953 (ttm) cc_final: 0.6715 (ttm) REVERT: p 1172 MET cc_start: 0.7269 (mmt) cc_final: 0.6321 (mmm) REVERT: q 61 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: q 83 GLN cc_start: 0.8357 (mt0) cc_final: 0.8109 (mt0) REVERT: q 93 PHE cc_start: 0.7527 (m-80) cc_final: 0.7179 (m-80) REVERT: s 108 GLN cc_start: 0.8204 (mt0) cc_final: 0.7998 (mt0) REVERT: s 133 GLN cc_start: 0.7842 (mt0) cc_final: 0.6382 (mm-40) REVERT: s 154 GLU cc_start: 0.7095 (pm20) cc_final: 0.6843 (pm20) REVERT: s 172 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6683 (mtt90) REVERT: s 203 TYR cc_start: 0.8488 (t80) cc_final: 0.7700 (t80) REVERT: t 57 MET cc_start: 0.7439 (ttp) cc_final: 0.7105 (ttm) REVERT: t 59 LYS cc_start: 0.6350 (ptpt) cc_final: 0.6145 (ptpp) REVERT: t 76 CYS cc_start: 0.7705 (t) cc_final: 0.7472 (m) REVERT: t 79 VAL cc_start: 0.7495 (t) cc_final: 0.7071 (p) REVERT: t 80 MET cc_start: 0.7174 (mmt) cc_final: 0.6197 (mmt) REVERT: t 86 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6891 (mp0) REVERT: t 87 THR cc_start: 0.8240 (p) cc_final: 0.8019 (p) REVERT: t 115 TYR cc_start: 0.8142 (p90) cc_final: 0.7797 (p90) REVERT: u 63 ARG cc_start: 0.7436 (mtp180) cc_final: 0.7157 (mtp180) REVERT: u 104 MET cc_start: 0.8880 (ttp) cc_final: 0.8214 (ppp) REVERT: u 157 ILE cc_start: 0.6995 (mt) cc_final: 0.6777 (mt) REVERT: u 164 MET cc_start: 0.2609 (mmt) cc_final: 0.2200 (mmt) REVERT: v 37 MET cc_start: 0.7983 (mtp) cc_final: 0.7708 (mtt) REVERT: v 63 THR cc_start: 0.9363 (p) cc_final: 0.9070 (t) REVERT: v 76 ASN cc_start: 0.8125 (m-40) cc_final: 0.7707 (t0) REVERT: v 100 GLU cc_start: 0.7700 (tt0) cc_final: 0.7251 (mt-10) REVERT: v 132 LEU cc_start: 0.8289 (mt) cc_final: 0.8084 (mt) REVERT: v 136 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7553 (mt-10) REVERT: v 146 LYS cc_start: 0.7651 (tttt) cc_final: 0.7119 (ttpp) REVERT: w 50 ASN cc_start: 0.7600 (t0) cc_final: 0.7213 (t0) REVERT: w 63 ASP cc_start: 0.8224 (p0) cc_final: 0.8006 (p0) REVERT: w 69 ILE cc_start: 0.8159 (mt) cc_final: 0.7719 (mt) REVERT: w 71 ASP cc_start: 0.8379 (m-30) cc_final: 0.8060 (m-30) REVERT: w 93 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7778 (tt0) REVERT: x 58 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7601 (mmmm) REVERT: x 62 TYR cc_start: 0.7879 (m-80) cc_final: 0.6939 (m-80) REVERT: y 16 GLU cc_start: 0.7196 (tt0) cc_final: 0.6685 (tt0) REVERT: y 27 VAL cc_start: 0.8447 (t) cc_final: 0.8119 (m) REVERT: y 48 SER cc_start: 0.8382 (t) cc_final: 0.8180 (m) REVERT: y 82 SER cc_start: 0.7542 (t) cc_final: 0.7012 (p) REVERT: z 35 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7406 (ttm-80) REVERT: z 56 ASP cc_start: 0.7466 (m-30) cc_final: 0.7186 (p0) outliers start: 94 outliers final: 61 residues processed: 693 average time/residue: 0.4973 time to fit residues: 548.8444 Evaluate side-chains 641 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 576 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 184 CYS Chi-restraints excluded: chain o residue 186 ARG Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 316 THR Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL 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 697 LYS Chi-restraints excluded: chain o residue 818 GLU Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1017 SER Chi-restraints excluded: chain o residue 1164 THR Chi-restraints excluded: chain o residue 1165 THR 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 p residue 36 GLU Chi-restraints excluded: chain p residue 51 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 260 LEU Chi-restraints excluded: chain p residue 263 ILE Chi-restraints excluded: chain p residue 273 PHE Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 524 LYS Chi-restraints excluded: chain p residue 539 SER Chi-restraints excluded: chain p residue 616 THR Chi-restraints excluded: chain p residue 633 LEU Chi-restraints excluded: chain p residue 841 ARG Chi-restraints excluded: chain p residue 910 THR Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 974 SER Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 61 ASP Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 197 SER Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 75 ILE Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 106 THR Chi-restraints excluded: chain w residue 12 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 42 LEU 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: 20.0000 chunk 260 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 383 optimal weight: 3.9990 chunk 413 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 341 GLN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 493 ASN o 671 ASN ** o 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 731 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 749 HIS p 980 HIS ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 232 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 24 ASN v 133 HIS ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 45 GLN ** w 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 100 HIS x 16 ASN ** y 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 84 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 36641 Z= 0.415 Angle : 0.582 11.872 49979 Z= 0.308 Chirality : 0.043 0.188 5567 Planarity : 0.004 0.054 6099 Dihedral : 16.683 142.743 5838 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.52 % Favored : 95.31 % Rotamer: Outliers : 3.66 % Allowed : 12.85 % Favored : 83.49 % 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: 0.45 (0.13), residues: 4137 helix: 1.42 (0.14), residues: 1402 sheet: -0.12 (0.20), residues: 646 loop : -0.27 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP o 479 HIS 0.028 0.002 HIS o 301 PHE 0.027 0.002 PHE u 107 TYR 0.019 0.002 TYR o 669 ARG 0.006 0.001 ARG q 193 *********************** 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 711 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 576 time to evaluate : 3.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 67 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8403 (ttm110) REVERT: o 192 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7703 (ptm-80) REVERT: o 197 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7545 (mp0) REVERT: o 201 GLU cc_start: 0.7891 (tt0) cc_final: 0.7657 (pt0) REVERT: o 321 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6878 (mp0) REVERT: o 437 ASP cc_start: 0.7460 (m-30) cc_final: 0.7257 (m-30) REVERT: o 451 CYS cc_start: 0.6928 (m) cc_final: 0.6510 (p) REVERT: o 687 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8775 (tp) REVERT: o 700 GLN cc_start: 0.7458 (tt0) cc_final: 0.6913 (tp-100) REVERT: o 712 ASP cc_start: 0.7305 (m-30) cc_final: 0.6890 (m-30) REVERT: o 726 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8140 (pp20) REVERT: o 803 LYS cc_start: 0.7730 (tttp) cc_final: 0.7020 (tptp) REVERT: o 824 GLU cc_start: 0.7662 (pt0) cc_final: 0.7288 (mp0) REVERT: o 868 MET cc_start: 0.7783 (ptt) cc_final: 0.7369 (ptm) REVERT: o 953 GLU cc_start: 0.7781 (tp30) cc_final: 0.7308 (tp30) REVERT: o 1128 ILE cc_start: 0.6822 (mm) cc_final: 0.6233 (tt) REVERT: o 1132 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8335 (mmtm) REVERT: o 1146 GLN cc_start: 0.8231 (pt0) cc_final: 0.7689 (pp30) REVERT: o 1212 LEU cc_start: 0.7591 (tp) cc_final: 0.7189 (tt) REVERT: o 1221 MET cc_start: 0.8639 (mmp) cc_final: 0.8191 (mmt) REVERT: o 1259 ILE cc_start: 0.8182 (mt) cc_final: 0.7904 (mt) REVERT: o 1282 ASP cc_start: 0.7804 (p0) cc_final: 0.7430 (p0) REVERT: o 1292 MET cc_start: 0.8328 (mtm) cc_final: 0.7808 (mmt) REVERT: o 1306 LYS cc_start: 0.7128 (mttt) cc_final: 0.6801 (mtpp) REVERT: o 1327 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: o 1329 LYS cc_start: 0.7535 (tttt) cc_final: 0.7335 (ttpp) REVERT: o 1344 MET cc_start: 0.6236 (tpp) cc_final: 0.5991 (tpt) REVERT: o 1351 ASP cc_start: 0.8231 (m-30) cc_final: 0.7887 (m-30) REVERT: o 1364 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6547 (mm-30) REVERT: o 1383 TYR cc_start: 0.7518 (t80) cc_final: 0.7110 (t80) REVERT: o 1422 GLN cc_start: 0.7246 (mt0) cc_final: 0.6313 (mm110) REVERT: o 1478 GLU cc_start: 0.7192 (tt0) cc_final: 0.6618 (tp30) REVERT: o 1484 MET cc_start: 0.4353 (tmm) cc_final: 0.3857 (tmm) REVERT: p 36 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: p 46 SER cc_start: 0.7450 (t) cc_final: 0.7155 (m) REVERT: p 141 GLN cc_start: 0.8541 (pt0) cc_final: 0.8283 (pm20) REVERT: p 143 GLN cc_start: 0.7250 (mp10) cc_final: 0.7043 (mp10) REVERT: p 144 HIS cc_start: 0.7953 (m-70) cc_final: 0.7678 (m170) REVERT: p 168 ASP cc_start: 0.7226 (p0) cc_final: 0.6732 (m-30) REVERT: p 238 SER cc_start: 0.7519 (OUTLIER) cc_final: 0.7020 (p) REVERT: p 324 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7704 (mmm-85) REVERT: p 344 GLN cc_start: 0.7906 (mt0) cc_final: 0.7448 (tt0) REVERT: p 580 PRO cc_start: 0.8151 (Cg_endo) cc_final: 0.7775 (Cg_exo) REVERT: p 584 MET cc_start: 0.7983 (mmm) cc_final: 0.7687 (tpt) REVERT: p 606 ASP cc_start: 0.6739 (t0) cc_final: 0.6214 (t0) REVERT: p 608 ARG cc_start: 0.6391 (ttp80) cc_final: 0.5981 (ttm-80) REVERT: p 630 LYS cc_start: 0.7498 (mttt) cc_final: 0.7269 (mmtm) REVERT: p 733 MET cc_start: 0.8325 (mtt) cc_final: 0.7894 (ttm) REVERT: p 815 LYS cc_start: 0.8733 (ptmm) cc_final: 0.8458 (ptmm) REVERT: p 1080 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7260 (mtp85) REVERT: p 1114 TYR cc_start: 0.7595 (t80) cc_final: 0.7233 (t80) REVERT: p 1121 LEU cc_start: 0.8239 (mt) cc_final: 0.7845 (mt) REVERT: q 158 GLU cc_start: 0.7823 (tt0) cc_final: 0.7442 (pt0) REVERT: q 210 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8022 (mm-30) REVERT: s 26 TYR cc_start: 0.7895 (m-80) cc_final: 0.7062 (m-80) REVERT: s 108 GLN cc_start: 0.8300 (mt0) cc_final: 0.7868 (mt0) REVERT: s 133 GLN cc_start: 0.8260 (mt0) cc_final: 0.7612 (mm-40) REVERT: s 154 GLU cc_start: 0.7133 (pm20) cc_final: 0.6731 (pm20) REVERT: s 166 ARG cc_start: 0.7158 (mtt180) cc_final: 0.6383 (mtm110) REVERT: t 59 LYS cc_start: 0.6357 (ptpt) cc_final: 0.6142 (ptpp) REVERT: t 79 VAL cc_start: 0.7365 (t) cc_final: 0.7017 (p) REVERT: t 80 MET cc_start: 0.7106 (mmt) cc_final: 0.6892 (mmt) REVERT: t 86 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6852 (mp0) REVERT: u 8 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7304 (mm-30) REVERT: u 10 GLU cc_start: 0.8009 (mp0) cc_final: 0.7786 (mp0) REVERT: u 63 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7185 (mtp180) REVERT: u 164 MET cc_start: 0.2703 (mmt) cc_final: 0.2302 (mmt) REVERT: v 4 ILE cc_start: 0.8558 (mt) cc_final: 0.8126 (mm) REVERT: v 37 MET cc_start: 0.7941 (mtp) cc_final: 0.7561 (mtt) REVERT: v 76 ASN cc_start: 0.8444 (m-40) cc_final: 0.8184 (t0) REVERT: v 95 LYS cc_start: 0.7142 (tttt) cc_final: 0.6654 (ttmm) REVERT: v 103 GLU cc_start: 0.8024 (pt0) cc_final: 0.7365 (pm20) REVERT: v 141 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8128 (p) REVERT: v 146 LYS cc_start: 0.7580 (tttt) cc_final: 0.7249 (tttp) REVERT: w 50 ASN cc_start: 0.7748 (t0) cc_final: 0.7375 (t0) REVERT: w 63 ASP cc_start: 0.8392 (p0) cc_final: 0.7753 (p0) REVERT: w 67 GLN cc_start: 0.8322 (mt0) cc_final: 0.7682 (mp10) REVERT: w 71 ASP cc_start: 0.8534 (m-30) cc_final: 0.8300 (m-30) REVERT: w 93 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7872 (mt-10) REVERT: x 48 MET cc_start: 0.8745 (mmp) cc_final: 0.8405 (mmt) REVERT: y 16 GLU cc_start: 0.7633 (tt0) cc_final: 0.7129 (tt0) REVERT: y 27 VAL cc_start: 0.8444 (t) cc_final: 0.8113 (m) REVERT: y 29 ASN cc_start: 0.7965 (m110) cc_final: 0.7640 (m110) REVERT: y 32 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6879 (tt) REVERT: y 48 SER cc_start: 0.8382 (t) cc_final: 0.8182 (m) REVERT: y 82 SER cc_start: 0.7703 (t) cc_final: 0.7131 (p) REVERT: y 84 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6907 (mp-120) REVERT: z 32 ASP cc_start: 0.8582 (t70) cc_final: 0.8239 (t0) REVERT: z 42 ARG cc_start: 0.8467 (mtp180) cc_final: 0.7816 (mtt90) REVERT: z 56 ASP cc_start: 0.7456 (m-30) cc_final: 0.7096 (p0) outliers start: 135 outliers final: 96 residues processed: 671 average time/residue: 0.5192 time to fit residues: 552.7702 Evaluate side-chains 641 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 538 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 41 ILE Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 186 ARG Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 316 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 406 VAL Chi-restraints excluded: chain o residue 439 HIS Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 535 MET Chi-restraints excluded: chain o residue 552 ASP Chi-restraints excluded: chain o residue 608 THR Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 818 GLU Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1017 SER Chi-restraints excluded: chain o residue 1024 ASN Chi-restraints excluded: chain o residue 1029 LEU Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1135 LYS Chi-restraints excluded: chain o residue 1164 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1235 ILE 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 1374 VAL Chi-restraints excluded: chain o residue 1410 HIS Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 238 SER Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 407 MET Chi-restraints excluded: chain p residue 422 PHE Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 466 VAL Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 480 SER Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 524 LYS Chi-restraints excluded: chain p residue 534 VAL Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 974 SER Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 79 GLU Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 137 ILE Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain s residue 197 SER Chi-restraints excluded: chain t residue 54 THR Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 95 LYS Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 72 ASP 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 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 25 THR Chi-restraints excluded: chain y residue 32 LEU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 77 THR Chi-restraints excluded: chain y residue 84 GLN Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 198 optimal weight: 0.0040 chunk 42 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 257 optimal weight: 0.0770 chunk 384 optimal weight: 0.9980 chunk 406 optimal weight: 0.0370 chunk 200 optimal weight: 0.0670 chunk 364 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN o 765 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 935 GLN ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o1263 ASN ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN p1133 HIS q 18 ASN ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 232 ASN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 41 ASN w 45 GLN ** w 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 84 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 36641 Z= 0.115 Angle : 0.431 9.852 49979 Z= 0.233 Chirality : 0.038 0.169 5567 Planarity : 0.003 0.037 6099 Dihedral : 16.500 140.558 5837 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 28.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.06 % Rotamer: Outliers : 2.33 % Allowed : 14.86 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4137 helix: 2.00 (0.14), residues: 1395 sheet: -0.05 (0.19), residues: 665 loop : -0.10 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP o 679 HIS 0.007 0.001 HIS p 842 PHE 0.085 0.001 PHE o 431 TYR 0.014 0.001 TYR o 669 ARG 0.010 0.000 ARG o 430 *********************** 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 647 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 561 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 67 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8451 (ttm110) REVERT: o 192 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7850 (ptm-80) REVERT: o 193 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8254 (ttp80) REVERT: o 197 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7539 (mp0) REVERT: o 321 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6868 (mp0) REVERT: o 451 CYS cc_start: 0.6815 (m) cc_final: 0.6318 (p) REVERT: o 561 MET cc_start: 0.7193 (mtt) cc_final: 0.6722 (mtp) REVERT: o 687 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8734 (tp) REVERT: o 700 GLN cc_start: 0.7457 (tt0) cc_final: 0.7062 (tp40) REVERT: o 712 ASP cc_start: 0.7233 (m-30) cc_final: 0.6820 (m-30) REVERT: o 726 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8124 (pp20) REVERT: o 803 LYS cc_start: 0.7751 (tttp) cc_final: 0.6707 (tptp) REVERT: o 824 GLU cc_start: 0.7664 (pt0) cc_final: 0.7283 (mp0) REVERT: o 953 GLU cc_start: 0.7733 (tp30) cc_final: 0.7360 (tp30) REVERT: o 1117 VAL cc_start: 0.6529 (t) cc_final: 0.6254 (p) REVERT: o 1128 ILE cc_start: 0.6753 (mm) cc_final: 0.6496 (tt) REVERT: o 1132 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8294 (mmtm) REVERT: o 1136 THR cc_start: 0.9017 (m) cc_final: 0.8737 (t) REVERT: o 1149 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8094 (mtm110) REVERT: o 1212 LEU cc_start: 0.7583 (tp) cc_final: 0.7245 (tt) REVERT: o 1259 ILE cc_start: 0.8004 (mt) cc_final: 0.7757 (mt) REVERT: o 1282 ASP cc_start: 0.7894 (p0) cc_final: 0.7520 (p0) REVERT: o 1292 MET cc_start: 0.8265 (mtm) cc_final: 0.7676 (mmt) REVERT: o 1296 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6880 (tpp) REVERT: o 1306 LYS cc_start: 0.7139 (mttt) cc_final: 0.6796 (mtpp) REVERT: o 1327 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6824 (tp30) REVERT: o 1351 ASP cc_start: 0.8115 (m-30) cc_final: 0.7880 (m-30) REVERT: o 1364 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6456 (mm-30) REVERT: o 1383 TYR cc_start: 0.7461 (t80) cc_final: 0.7065 (t80) REVERT: o 1422 GLN cc_start: 0.7167 (mt0) cc_final: 0.6466 (mm-40) REVERT: o 1478 GLU cc_start: 0.7158 (tt0) cc_final: 0.6601 (tp30) REVERT: o 1484 MET cc_start: 0.4243 (tmm) cc_final: 0.3701 (tmm) REVERT: p 46 SER cc_start: 0.7278 (t) cc_final: 0.6976 (m) REVERT: p 141 GLN cc_start: 0.8495 (pt0) cc_final: 0.8226 (pm20) REVERT: p 143 GLN cc_start: 0.7389 (mp10) cc_final: 0.7139 (mp10) REVERT: p 144 HIS cc_start: 0.7964 (m-70) cc_final: 0.7666 (m170) REVERT: p 168 ASP cc_start: 0.7080 (p0) cc_final: 0.6588 (m-30) REVERT: p 309 PHE cc_start: 0.8528 (t80) cc_final: 0.8078 (t80) REVERT: p 324 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7444 (mmm-85) REVERT: p 341 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6782 (tm-30) REVERT: p 344 GLN cc_start: 0.7849 (mt0) cc_final: 0.7618 (tt0) REVERT: p 546 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7264 (mm-30) REVERT: p 580 PRO cc_start: 0.8112 (Cg_endo) cc_final: 0.7819 (Cg_exo) REVERT: p 606 ASP cc_start: 0.6632 (t0) cc_final: 0.6203 (t0) REVERT: p 630 LYS cc_start: 0.7482 (mttt) cc_final: 0.7248 (mmtm) REVERT: p 733 MET cc_start: 0.8368 (mtt) cc_final: 0.8020 (mtm) REVERT: p 863 ASP cc_start: 0.7967 (m-30) cc_final: 0.6954 (t0) REVERT: p 1022 LEU cc_start: 0.7384 (mt) cc_final: 0.7145 (tp) REVERT: p 1080 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7055 (mtp85) REVERT: p 1109 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6761 (mt-10) REVERT: p 1114 TYR cc_start: 0.7313 (t80) cc_final: 0.7070 (t80) REVERT: p 1121 LEU cc_start: 0.8204 (mt) cc_final: 0.7892 (mt) REVERT: q 158 GLU cc_start: 0.7734 (tt0) cc_final: 0.7402 (pt0) REVERT: q 210 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8121 (mm-30) REVERT: s 26 TYR cc_start: 0.7994 (m-80) cc_final: 0.6987 (m-80) REVERT: s 108 GLN cc_start: 0.8251 (mt0) cc_final: 0.7855 (mt0) REVERT: s 133 GLN cc_start: 0.8187 (mt0) cc_final: 0.7374 (mm-40) REVERT: s 154 GLU cc_start: 0.7136 (pm20) cc_final: 0.6723 (pm20) REVERT: s 159 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7742 (tp) REVERT: s 166 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6610 (mtm110) REVERT: t 79 VAL cc_start: 0.7300 (t) cc_final: 0.6926 (p) REVERT: t 86 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6822 (mp0) REVERT: t 115 TYR cc_start: 0.8017 (p90) cc_final: 0.7500 (p90) REVERT: u 10 GLU cc_start: 0.8043 (mp0) cc_final: 0.7827 (mp0) REVERT: u 164 MET cc_start: 0.2584 (mmt) cc_final: 0.2239 (mmt) REVERT: v 4 ILE cc_start: 0.8535 (mt) cc_final: 0.8105 (mm) REVERT: v 37 MET cc_start: 0.7913 (mtp) cc_final: 0.7518 (mtt) REVERT: v 76 ASN cc_start: 0.8284 (m-40) cc_final: 0.7991 (t0) REVERT: v 84 ARG cc_start: 0.7470 (mtt180) cc_final: 0.6681 (mtt180) REVERT: v 95 LYS cc_start: 0.6973 (tttt) cc_final: 0.6416 (ttmm) REVERT: v 133 HIS cc_start: 0.7578 (m-70) cc_final: 0.7217 (m-70) REVERT: v 146 LYS cc_start: 0.7579 (tttt) cc_final: 0.7065 (ttpp) REVERT: w 15 ARG cc_start: 0.7807 (ptp90) cc_final: 0.7023 (ptp90) REVERT: w 50 ASN cc_start: 0.7620 (t0) cc_final: 0.7385 (t0) REVERT: w 63 ASP cc_start: 0.8396 (p0) cc_final: 0.8047 (p0) REVERT: w 71 ASP cc_start: 0.8643 (m-30) cc_final: 0.8341 (m-30) REVERT: w 93 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7781 (tt0) REVERT: x 48 MET cc_start: 0.8766 (mmp) cc_final: 0.8422 (mmt) REVERT: y 16 GLU cc_start: 0.7546 (tt0) cc_final: 0.7099 (tt0) REVERT: y 27 VAL cc_start: 0.8388 (t) cc_final: 0.8103 (m) REVERT: y 29 ASN cc_start: 0.7748 (m110) cc_final: 0.7535 (m-40) REVERT: y 48 SER cc_start: 0.8319 (t) cc_final: 0.8116 (m) REVERT: y 82 SER cc_start: 0.7672 (OUTLIER) cc_final: 0.7101 (p) REVERT: z 32 ASP cc_start: 0.8576 (t70) cc_final: 0.8171 (t0) REVERT: z 42 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7837 (mmm-85) REVERT: z 56 ASP cc_start: 0.7403 (m-30) cc_final: 0.6983 (p0) outliers start: 86 outliers final: 51 residues processed: 612 average time/residue: 0.5199 time to fit residues: 504.9005 Evaluate side-chains 593 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 537 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 186 ARG Chi-restraints excluded: chain o residue 187 TYR Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 431 PHE Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 552 ASP 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 697 LYS Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1235 ILE Chi-restraints excluded: chain o residue 1296 MET Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1374 VAL Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 260 LEU Chi-restraints excluded: chain p residue 266 GLU Chi-restraints excluded: chain p residue 273 PHE Chi-restraints excluded: chain p residue 422 PHE Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 609 GLU Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain p residue 1143 LYS Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 49 SER Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain w residue 41 ASN Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 82 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 0.1980 chunk 231 optimal weight: 0.4980 chunk 5 optimal weight: 30.0000 chunk 302 optimal weight: 2.9990 chunk 167 optimal weight: 0.0370 chunk 347 optimal weight: 0.5980 chunk 281 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 365 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 45 GLN w 91 HIS w 98 GLN y 29 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36641 Z= 0.135 Angle : 0.420 10.120 49979 Z= 0.226 Chirality : 0.038 0.167 5567 Planarity : 0.003 0.040 6099 Dihedral : 16.378 137.106 5837 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 29.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 2.44 % Allowed : 14.97 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.13), residues: 4137 helix: 2.24 (0.14), residues: 1395 sheet: 0.04 (0.19), residues: 675 loop : -0.06 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 679 HIS 0.005 0.001 HIS u 4 PHE 0.080 0.001 PHE o 431 TYR 0.013 0.001 TYR w 54 ARG 0.009 0.000 ARG w 40 *********************** 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 648 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 558 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 45 GLU cc_start: 0.8015 (mp0) cc_final: 0.7129 (pm20) REVERT: o 66 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8279 (mp0) REVERT: o 67 ARG cc_start: 0.8748 (ttp80) cc_final: 0.8473 (ttm110) REVERT: o 321 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6837 (mp0) REVERT: o 451 CYS cc_start: 0.6871 (m) cc_final: 0.6357 (p) REVERT: o 687 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8761 (tp) REVERT: o 700 GLN cc_start: 0.7543 (tt0) cc_final: 0.7164 (tp40) REVERT: o 712 ASP cc_start: 0.7231 (m-30) cc_final: 0.6813 (m-30) REVERT: o 803 LYS cc_start: 0.7676 (tttp) cc_final: 0.6950 (tptp) REVERT: o 824 GLU cc_start: 0.7706 (pt0) cc_final: 0.7310 (mp0) REVERT: o 868 MET cc_start: 0.7864 (ptt) cc_final: 0.7448 (ptm) REVERT: o 953 GLU cc_start: 0.7758 (tp30) cc_final: 0.7373 (tp30) REVERT: o 1117 VAL cc_start: 0.6518 (t) cc_final: 0.6253 (p) REVERT: o 1128 ILE cc_start: 0.6693 (mm) cc_final: 0.6360 (tt) REVERT: o 1132 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8308 (mmtm) REVERT: o 1136 THR cc_start: 0.9026 (m) cc_final: 0.8740 (t) REVERT: o 1149 ARG cc_start: 0.8552 (mtm110) cc_final: 0.8160 (mtm110) REVERT: o 1212 LEU cc_start: 0.7576 (tp) cc_final: 0.7253 (tt) REVERT: o 1259 ILE cc_start: 0.8064 (mt) cc_final: 0.7833 (mt) REVERT: o 1282 ASP cc_start: 0.7869 (p0) cc_final: 0.7488 (p0) REVERT: o 1292 MET cc_start: 0.8251 (mtm) cc_final: 0.7679 (mmt) REVERT: o 1296 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6741 (tpp) REVERT: o 1306 LYS cc_start: 0.7152 (mttt) cc_final: 0.6795 (mtpp) REVERT: o 1327 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: o 1351 ASP cc_start: 0.8014 (m-30) cc_final: 0.7788 (m-30) REVERT: o 1364 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6488 (mm-30) REVERT: o 1383 TYR cc_start: 0.7465 (t80) cc_final: 0.7066 (t80) REVERT: o 1422 GLN cc_start: 0.7124 (mt0) cc_final: 0.6445 (mm-40) REVERT: o 1478 GLU cc_start: 0.7191 (tt0) cc_final: 0.6634 (tp30) REVERT: p 46 SER cc_start: 0.7305 (t) cc_final: 0.6977 (m) REVERT: p 141 GLN cc_start: 0.8490 (pt0) cc_final: 0.8230 (pm20) REVERT: p 143 GLN cc_start: 0.7386 (mp10) cc_final: 0.7151 (mp10) REVERT: p 144 HIS cc_start: 0.7950 (m-70) cc_final: 0.7678 (m170) REVERT: p 168 ASP cc_start: 0.7159 (p0) cc_final: 0.6754 (m-30) REVERT: p 169 ARG cc_start: 0.7417 (tmm-80) cc_final: 0.6804 (mmp80) REVERT: p 297 MET cc_start: 0.6930 (mtp) cc_final: 0.6697 (tpp) REVERT: p 324 ARG cc_start: 0.7876 (mtt90) cc_final: 0.7494 (mmm-85) REVERT: p 333 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6929 (tm-30) REVERT: p 341 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6736 (tm-30) REVERT: p 344 GLN cc_start: 0.7839 (mt0) cc_final: 0.7614 (tt0) REVERT: p 346 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6699 (mt-10) REVERT: p 528 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8101 (mt) REVERT: p 580 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7802 (Cg_exo) REVERT: p 606 ASP cc_start: 0.6633 (t0) cc_final: 0.6218 (t0) REVERT: p 630 LYS cc_start: 0.7500 (mttt) cc_final: 0.7283 (mmtm) REVERT: p 733 MET cc_start: 0.8375 (mtt) cc_final: 0.7934 (ttm) REVERT: p 863 ASP cc_start: 0.7992 (m-30) cc_final: 0.7003 (t0) REVERT: p 916 TYR cc_start: 0.5484 (m-10) cc_final: 0.5064 (m-80) REVERT: p 1022 LEU cc_start: 0.7493 (mt) cc_final: 0.7253 (tp) REVERT: p 1080 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7063 (mtp85) REVERT: p 1121 LEU cc_start: 0.8233 (mt) cc_final: 0.7916 (mt) REVERT: q 158 GLU cc_start: 0.7723 (tt0) cc_final: 0.7425 (pt0) REVERT: q 210 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8127 (mm-30) REVERT: s 26 TYR cc_start: 0.8011 (m-80) cc_final: 0.7224 (m-80) REVERT: s 72 MET cc_start: 0.7723 (ttt) cc_final: 0.6890 (ttp) REVERT: s 108 GLN cc_start: 0.8255 (mt0) cc_final: 0.7878 (mt0) REVERT: s 133 GLN cc_start: 0.8139 (mt0) cc_final: 0.7641 (mm-40) REVERT: s 154 GLU cc_start: 0.7143 (pm20) cc_final: 0.6716 (pm20) REVERT: s 159 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7718 (tp) REVERT: s 166 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6609 (mtm110) REVERT: t 79 VAL cc_start: 0.7291 (t) cc_final: 0.6906 (p) REVERT: t 86 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6852 (mp0) REVERT: t 115 TYR cc_start: 0.8026 (p90) cc_final: 0.7545 (p90) REVERT: u 10 GLU cc_start: 0.8054 (mp0) cc_final: 0.7849 (mp0) REVERT: u 164 MET cc_start: 0.2462 (mmt) cc_final: 0.2136 (mmt) REVERT: v 4 ILE cc_start: 0.8541 (mt) cc_final: 0.8112 (mm) REVERT: v 37 MET cc_start: 0.7882 (mtp) cc_final: 0.7549 (mtt) REVERT: v 76 ASN cc_start: 0.8195 (m-40) cc_final: 0.7827 (t0) REVERT: v 95 LYS cc_start: 0.6981 (tttt) cc_final: 0.6426 (ttmm) REVERT: v 133 HIS cc_start: 0.7581 (m-70) cc_final: 0.7224 (m-70) REVERT: v 146 LYS cc_start: 0.7453 (tttt) cc_final: 0.6927 (ttpp) REVERT: w 15 ARG cc_start: 0.7812 (ptp90) cc_final: 0.6877 (ptp90) REVERT: w 50 ASN cc_start: 0.7635 (t0) cc_final: 0.7416 (t0) REVERT: w 63 ASP cc_start: 0.8403 (p0) cc_final: 0.8138 (p0) REVERT: w 71 ASP cc_start: 0.8606 (m-30) cc_final: 0.8345 (m-30) REVERT: w 93 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7771 (tt0) REVERT: y 16 GLU cc_start: 0.7609 (tt0) cc_final: 0.7213 (tt0) REVERT: y 27 VAL cc_start: 0.8390 (t) cc_final: 0.8104 (m) REVERT: y 29 ASN cc_start: 0.7825 (m-40) cc_final: 0.7525 (m110) REVERT: y 82 SER cc_start: 0.7642 (t) cc_final: 0.7065 (p) REVERT: z 35 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7262 (ttm170) outliers start: 90 outliers final: 68 residues processed: 612 average time/residue: 0.5133 time to fit residues: 500.0365 Evaluate side-chains 611 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 538 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 431 PHE Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 552 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1164 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1235 ILE Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1296 MET Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1374 VAL Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 260 LEU Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 273 PHE Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 422 PHE Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 516 GLU Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain p residue 1140 CYS Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain t residue 95 LYS Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 71 ILE Chi-restraints excluded: chain y residue 114 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 3.9990 chunk 366 optimal weight: 50.0000 chunk 80 optimal weight: 2.9990 chunk 238 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 407 optimal weight: 0.9990 chunk 338 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN ** o 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS t 46 GLN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 45 GLN y 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36641 Z= 0.329 Angle : 0.513 10.430 49979 Z= 0.270 Chirality : 0.041 0.173 5567 Planarity : 0.004 0.045 6099 Dihedral : 16.386 130.115 5837 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 29.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.10 % Favored : 94.78 % Rotamer: Outliers : 3.34 % Allowed : 14.48 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 4137 helix: 1.93 (0.14), residues: 1393 sheet: -0.02 (0.19), residues: 682 loop : -0.19 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 479 HIS 0.006 0.001 HIS w 100 PHE 0.078 0.002 PHE o 431 TYR 0.020 0.002 TYR o 669 ARG 0.010 0.000 ARG o 192 *********************** 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 657 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 534 time to evaluate : 3.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: o 45 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: o 66 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8297 (mp0) REVERT: o 67 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8406 (ttm110) REVERT: o 197 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7696 (mp0) REVERT: o 321 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6811 (mp0) REVERT: o 451 CYS cc_start: 0.6878 (m) cc_final: 0.6399 (p) REVERT: o 508 SER cc_start: 0.6787 (t) cc_final: 0.6347 (m) REVERT: o 687 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8836 (tp) REVERT: o 700 GLN cc_start: 0.7558 (tt0) cc_final: 0.7195 (tp40) REVERT: o 712 ASP cc_start: 0.7219 (m-30) cc_final: 0.6824 (m-30) REVERT: o 803 LYS cc_start: 0.7624 (tttp) cc_final: 0.7051 (tptp) REVERT: o 824 GLU cc_start: 0.7879 (pt0) cc_final: 0.7523 (mp0) REVERT: o 953 GLU cc_start: 0.7826 (tp30) cc_final: 0.7357 (tp30) REVERT: o 1117 VAL cc_start: 0.6611 (t) cc_final: 0.6273 (p) REVERT: o 1128 ILE cc_start: 0.6781 (mm) cc_final: 0.6432 (tt) REVERT: o 1132 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8393 (mmtm) REVERT: o 1212 LEU cc_start: 0.7550 (tp) cc_final: 0.7218 (tt) REVERT: o 1282 ASP cc_start: 0.7809 (p0) cc_final: 0.7455 (p0) REVERT: o 1306 LYS cc_start: 0.7191 (mttt) cc_final: 0.6835 (mtpp) REVERT: o 1327 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: o 1351 ASP cc_start: 0.8166 (m-30) cc_final: 0.7895 (m-30) REVERT: o 1364 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6590 (mm-30) REVERT: o 1422 GLN cc_start: 0.7182 (mt0) cc_final: 0.6343 (mm-40) REVERT: o 1478 GLU cc_start: 0.7344 (tt0) cc_final: 0.6745 (tp30) REVERT: o 1484 MET cc_start: 0.3903 (tmm) cc_final: 0.2479 (ppp) REVERT: p 46 SER cc_start: 0.7388 (t) cc_final: 0.7054 (m) REVERT: p 141 GLN cc_start: 0.8523 (pt0) cc_final: 0.8226 (pm20) REVERT: p 143 GLN cc_start: 0.7405 (mp10) cc_final: 0.7166 (mp10) REVERT: p 144 HIS cc_start: 0.7714 (m-70) cc_final: 0.7411 (m170) REVERT: p 156 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7529 (mp) REVERT: p 168 ASP cc_start: 0.7007 (p0) cc_final: 0.6627 (m-30) REVERT: p 169 ARG cc_start: 0.7439 (tmm-80) cc_final: 0.6843 (mmp80) REVERT: p 238 SER cc_start: 0.7559 (OUTLIER) cc_final: 0.6928 (p) REVERT: p 297 MET cc_start: 0.6972 (mtp) cc_final: 0.6599 (tpp) REVERT: p 315 ASN cc_start: 0.8303 (m-40) cc_final: 0.8085 (m-40) REVERT: p 324 ARG cc_start: 0.8111 (mtt90) cc_final: 0.7775 (mmm-85) REVERT: p 333 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6965 (tm-30) REVERT: p 341 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6525 (tm-30) REVERT: p 344 GLN cc_start: 0.7904 (mt0) cc_final: 0.7688 (tt0) REVERT: p 345 LYS cc_start: 0.7138 (mptt) cc_final: 0.6548 (mttp) REVERT: p 346 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6638 (mt-10) REVERT: p 388 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: p 606 ASP cc_start: 0.6750 (t0) cc_final: 0.6325 (t0) REVERT: p 630 LYS cc_start: 0.7817 (mttt) cc_final: 0.7596 (mmtm) REVERT: p 733 MET cc_start: 0.8289 (mtt) cc_final: 0.8014 (mtm) REVERT: p 828 VAL cc_start: 0.7546 (t) cc_final: 0.7119 (p) REVERT: p 863 ASP cc_start: 0.8204 (m-30) cc_final: 0.7322 (t0) REVERT: p 916 TYR cc_start: 0.5540 (m-10) cc_final: 0.5120 (m-80) REVERT: p 1080 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7126 (mtp85) REVERT: p 1109 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6873 (mp0) REVERT: p 1121 LEU cc_start: 0.8255 (mt) cc_final: 0.7954 (mt) REVERT: q 158 GLU cc_start: 0.7661 (tt0) cc_final: 0.7406 (pt0) REVERT: q 210 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8199 (mm-30) REVERT: s 44 PHE cc_start: 0.5841 (m-80) cc_final: 0.5624 (m-80) REVERT: s 108 GLN cc_start: 0.8217 (mt0) cc_final: 0.7907 (mt0) REVERT: s 133 GLN cc_start: 0.8337 (mt0) cc_final: 0.7838 (mm-40) REVERT: s 154 GLU cc_start: 0.7198 (pm20) cc_final: 0.6789 (pm20) REVERT: s 159 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7800 (tp) REVERT: s 166 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6516 (mtm110) REVERT: t 79 VAL cc_start: 0.7308 (t) cc_final: 0.6931 (p) REVERT: t 115 TYR cc_start: 0.7998 (p90) cc_final: 0.7469 (p90) REVERT: u 164 MET cc_start: 0.2620 (mmt) cc_final: 0.2269 (mmt) REVERT: v 4 ILE cc_start: 0.8550 (mt) cc_final: 0.8107 (mm) REVERT: v 37 MET cc_start: 0.7899 (mtp) cc_final: 0.7573 (mtt) REVERT: v 76 ASN cc_start: 0.8328 (m-40) cc_final: 0.8038 (t0) REVERT: v 95 LYS cc_start: 0.7068 (tttt) cc_final: 0.6432 (ttmm) REVERT: v 133 HIS cc_start: 0.7977 (m-70) cc_final: 0.7647 (m-70) REVERT: v 146 LYS cc_start: 0.7506 (tttt) cc_final: 0.7068 (tttp) REVERT: w 15 ARG cc_start: 0.7825 (ptp90) cc_final: 0.6886 (ptp90) REVERT: w 50 ASN cc_start: 0.7719 (t0) cc_final: 0.7503 (t0) REVERT: w 63 ASP cc_start: 0.8496 (p0) cc_final: 0.8221 (p0) REVERT: w 71 ASP cc_start: 0.8630 (m-30) cc_final: 0.8423 (m-30) REVERT: w 93 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7843 (tt0) REVERT: x 48 MET cc_start: 0.8769 (mmp) cc_final: 0.8435 (mmt) REVERT: y 16 GLU cc_start: 0.7883 (tt0) cc_final: 0.7450 (tt0) REVERT: y 27 VAL cc_start: 0.8414 (t) cc_final: 0.8052 (m) REVERT: y 29 ASN cc_start: 0.7915 (m-40) cc_final: 0.7575 (m110) REVERT: y 82 SER cc_start: 0.7597 (t) cc_final: 0.7117 (p) REVERT: z 42 ARG cc_start: 0.8350 (mtp180) cc_final: 0.7901 (mmm-85) REVERT: z 56 ASP cc_start: 0.7643 (m-30) cc_final: 0.6994 (p0) outliers start: 123 outliers final: 104 residues processed: 613 average time/residue: 0.5070 time to fit residues: 495.5065 Evaluate side-chains 625 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 514 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 316 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 382 ARG Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 431 PHE Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 495 ASP Chi-restraints excluded: chain o residue 552 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 697 LYS Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1002 SER Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1135 LYS Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1164 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1235 ILE Chi-restraints excluded: chain o residue 1257 LEU Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1289 GLU 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 1374 VAL Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 156 LEU 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 272 VAL Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 403 LEU Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 524 LYS Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 602 SER Chi-restraints excluded: chain p residue 633 LEU Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 786 THR Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain p residue 1075 MET Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 34 ASN Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 79 GLU Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain s residue 197 SER Chi-restraints excluded: chain t residue 95 LYS Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 63 THR 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 113 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 22 ASN Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 114 GLU Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 297 optimal weight: 0.5980 chunk 230 optimal weight: 0.0370 chunk 342 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 405 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 247 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 372 ASN o 671 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 45 GLN y 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36641 Z= 0.166 Angle : 0.431 10.029 49979 Z= 0.231 Chirality : 0.039 0.167 5567 Planarity : 0.003 0.033 6099 Dihedral : 16.306 123.657 5837 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 29.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.35 % Favored : 95.53 % Rotamer: Outliers : 2.82 % Allowed : 15.43 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4137 helix: 2.19 (0.15), residues: 1390 sheet: 0.05 (0.19), residues: 672 loop : -0.17 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 679 HIS 0.004 0.001 HIS u 4 PHE 0.075 0.001 PHE o 431 TYR 0.014 0.001 TYR o 669 ARG 0.004 0.000 ARG o 334 *********************** 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 630 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 526 time to evaluate : 4.093 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 45 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: o 66 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8254 (mp0) REVERT: o 67 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8473 (ttm110) REVERT: o 192 ARG cc_start: 0.7198 (ptt90) cc_final: 0.6889 (ptt90) REVERT: o 197 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7681 (mp0) REVERT: o 321 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6725 (mp0) REVERT: o 448 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.7026 (ptt-90) REVERT: o 451 CYS cc_start: 0.6923 (m) cc_final: 0.6453 (p) REVERT: o 556 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: o 687 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8850 (tp) REVERT: o 700 GLN cc_start: 0.7582 (tt0) cc_final: 0.7346 (tp-100) REVERT: o 712 ASP cc_start: 0.7243 (m-30) cc_final: 0.6830 (m-30) REVERT: o 803 LYS cc_start: 0.7664 (tttp) cc_final: 0.6947 (tptp) REVERT: o 824 GLU cc_start: 0.7919 (pt0) cc_final: 0.7555 (mp0) REVERT: o 868 MET cc_start: 0.7686 (ptt) cc_final: 0.7351 (ptm) REVERT: o 953 GLU cc_start: 0.7825 (tp30) cc_final: 0.7411 (tp30) REVERT: o 1117 VAL cc_start: 0.6600 (t) cc_final: 0.6343 (p) REVERT: o 1128 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6387 (tt) REVERT: o 1132 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8342 (mmtm) REVERT: o 1136 THR cc_start: 0.9019 (m) cc_final: 0.8739 (t) REVERT: o 1146 GLN cc_start: 0.8329 (pt0) cc_final: 0.7827 (pp30) REVERT: o 1282 ASP cc_start: 0.7888 (p0) cc_final: 0.7523 (p0) REVERT: o 1306 LYS cc_start: 0.7196 (mttt) cc_final: 0.6828 (mtpp) REVERT: o 1327 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: o 1351 ASP cc_start: 0.8053 (m-30) cc_final: 0.7813 (m-30) REVERT: o 1364 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6529 (mm-30) REVERT: o 1396 ARG cc_start: 0.6959 (mtt-85) cc_final: 0.6474 (mtt-85) REVERT: o 1422 GLN cc_start: 0.6990 (mt0) cc_final: 0.6424 (mm-40) REVERT: o 1478 GLU cc_start: 0.7326 (tt0) cc_final: 0.6758 (tp30) REVERT: o 1484 MET cc_start: 0.4059 (tmm) cc_final: 0.3642 (tmm) REVERT: p 46 SER cc_start: 0.7291 (t) cc_final: 0.6944 (m) REVERT: p 141 GLN cc_start: 0.8528 (pt0) cc_final: 0.8214 (pm20) REVERT: p 143 GLN cc_start: 0.7398 (mp10) cc_final: 0.7148 (mp10) REVERT: p 144 HIS cc_start: 0.7729 (m-70) cc_final: 0.7415 (m170) REVERT: p 168 ASP cc_start: 0.6969 (p0) cc_final: 0.6616 (m-30) REVERT: p 169 ARG cc_start: 0.7413 (tmm-80) cc_final: 0.6817 (mmp80) REVERT: p 309 PHE cc_start: 0.8510 (t80) cc_final: 0.8266 (t80) REVERT: p 324 ARG cc_start: 0.8213 (mtt90) cc_final: 0.7794 (mmm-85) REVERT: p 333 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6996 (tm-30) REVERT: p 341 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6492 (tm-30) REVERT: p 344 GLN cc_start: 0.7881 (mt0) cc_final: 0.7495 (tt0) REVERT: p 345 LYS cc_start: 0.7160 (mptt) cc_final: 0.6637 (mttp) REVERT: p 346 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6567 (mt-10) REVERT: p 388 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: p 528 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8086 (mt) REVERT: p 550 MET cc_start: 0.7255 (ttp) cc_final: 0.6090 (tmm) REVERT: p 606 ASP cc_start: 0.6466 (t0) cc_final: 0.6044 (t0) REVERT: p 630 LYS cc_start: 0.7822 (mttt) cc_final: 0.7581 (mmtm) REVERT: p 733 MET cc_start: 0.8296 (mtt) cc_final: 0.8004 (ttm) REVERT: p 828 VAL cc_start: 0.7465 (t) cc_final: 0.7060 (p) REVERT: p 863 ASP cc_start: 0.8076 (m-30) cc_final: 0.7201 (t0) REVERT: p 916 TYR cc_start: 0.5603 (m-10) cc_final: 0.5198 (m-80) REVERT: p 1022 LEU cc_start: 0.7536 (mt) cc_final: 0.7306 (tp) REVERT: p 1080 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7078 (mtp85) REVERT: p 1109 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7028 (mp0) REVERT: p 1121 LEU cc_start: 0.8266 (mt) cc_final: 0.7961 (mt) REVERT: q 158 GLU cc_start: 0.7590 (tt0) cc_final: 0.7363 (pt0) REVERT: q 210 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8207 (mm-30) REVERT: s 26 TYR cc_start: 0.8124 (m-80) cc_final: 0.7345 (m-80) REVERT: s 44 PHE cc_start: 0.5814 (m-80) cc_final: 0.5591 (m-80) REVERT: s 72 MET cc_start: 0.7997 (ttt) cc_final: 0.7077 (ttp) REVERT: s 108 GLN cc_start: 0.8175 (mt0) cc_final: 0.7864 (mt0) REVERT: s 133 GLN cc_start: 0.8294 (mt0) cc_final: 0.7791 (mm-40) REVERT: s 154 GLU cc_start: 0.7180 (pm20) cc_final: 0.6771 (pm20) REVERT: s 159 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7785 (tp) REVERT: s 166 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6490 (mtm110) REVERT: t 79 VAL cc_start: 0.7263 (t) cc_final: 0.7044 (p) REVERT: t 115 TYR cc_start: 0.8037 (p90) cc_final: 0.7465 (p90) REVERT: u 164 MET cc_start: 0.2591 (mmt) cc_final: 0.2270 (mmt) REVERT: v 4 ILE cc_start: 0.8544 (mt) cc_final: 0.8096 (mm) REVERT: v 37 MET cc_start: 0.7908 (mtp) cc_final: 0.7612 (mtt) REVERT: v 76 ASN cc_start: 0.8317 (m-40) cc_final: 0.8034 (t0) REVERT: v 95 LYS cc_start: 0.7048 (tttt) cc_final: 0.6446 (ttmm) REVERT: v 133 HIS cc_start: 0.7960 (m-70) cc_final: 0.7631 (m-70) REVERT: v 146 LYS cc_start: 0.7498 (tttt) cc_final: 0.7030 (ttpp) REVERT: w 15 ARG cc_start: 0.7846 (ptp90) cc_final: 0.6856 (ptp90) REVERT: w 29 ASP cc_start: 0.6092 (t0) cc_final: 0.5781 (t0) REVERT: w 50 ASN cc_start: 0.7722 (t0) cc_final: 0.7518 (t0) REVERT: w 63 ASP cc_start: 0.8465 (p0) cc_final: 0.8181 (p0) REVERT: w 71 ASP cc_start: 0.8675 (m-30) cc_final: 0.8435 (m-30) REVERT: w 93 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7836 (tt0) REVERT: x 48 MET cc_start: 0.8780 (mmp) cc_final: 0.8429 (mmt) REVERT: y 16 GLU cc_start: 0.7693 (tt0) cc_final: 0.7252 (tt0) REVERT: y 23 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7136 (tptt) REVERT: y 27 VAL cc_start: 0.8356 (t) cc_final: 0.7980 (m) REVERT: y 29 ASN cc_start: 0.7932 (m-40) cc_final: 0.7603 (m110) REVERT: y 82 SER cc_start: 0.7641 (OUTLIER) cc_final: 0.7136 (p) REVERT: z 35 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7240 (ttm170) outliers start: 104 outliers final: 81 residues processed: 596 average time/residue: 0.5205 time to fit residues: 494.6130 Evaluate side-chains 611 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 519 time to evaluate : 4.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 406 VAL Chi-restraints excluded: chain o residue 448 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 552 ASP Chi-restraints excluded: chain o residue 556 GLU Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 697 LYS Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1164 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1235 ILE Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1289 GLU Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1374 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 422 PHE Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 563 ASP Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 602 SER Chi-restraints excluded: chain p residue 633 LEU Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain p residue 1075 MET Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 254 LYS Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 63 THR Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 23 LYS Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 82 SER Chi-restraints excluded: chain y residue 114 GLU Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 276 optimal weight: 0.0670 chunk 200 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 chunk 318 optimal weight: 0.0040 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 671 ASN ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 631 GLN ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 45 GLN y 89 ASN z 23 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36641 Z= 0.198 Angle : 0.442 10.022 49979 Z= 0.235 Chirality : 0.039 0.166 5567 Planarity : 0.003 0.046 6099 Dihedral : 16.245 113.966 5837 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 2.96 % Allowed : 15.35 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 4137 helix: 2.25 (0.15), residues: 1382 sheet: 0.06 (0.19), residues: 683 loop : -0.17 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 679 HIS 0.004 0.001 HIS w 100 PHE 0.102 0.001 PHE o 431 TYR 0.014 0.001 TYR o 669 ARG 0.005 0.000 ARG o 430 *********************** 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 625 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 516 time to evaluate : 3.836 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 45 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7124 (pm20) REVERT: o 66 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8255 (mp0) REVERT: o 67 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8482 (ttm110) REVERT: o 192 ARG cc_start: 0.7052 (ptt90) cc_final: 0.6739 (ptt90) REVERT: o 197 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7675 (mp0) REVERT: o 321 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6735 (mp0) REVERT: o 448 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.7035 (ptt-90) REVERT: o 451 CYS cc_start: 0.6968 (m) cc_final: 0.6489 (p) REVERT: o 687 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8883 (tp) REVERT: o 700 GLN cc_start: 0.7588 (tt0) cc_final: 0.7387 (tp40) REVERT: o 712 ASP cc_start: 0.7137 (m-30) cc_final: 0.6735 (m-30) REVERT: o 803 LYS cc_start: 0.7673 (tttp) cc_final: 0.7061 (tptp) REVERT: o 824 GLU cc_start: 0.7928 (pt0) cc_final: 0.7645 (mp0) REVERT: o 868 MET cc_start: 0.7693 (ptt) cc_final: 0.7358 (ptm) REVERT: o 953 GLU cc_start: 0.7858 (tp30) cc_final: 0.7445 (tp30) REVERT: o 1117 VAL cc_start: 0.6613 (t) cc_final: 0.6373 (p) REVERT: o 1128 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6406 (tt) REVERT: o 1132 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8354 (mmtm) REVERT: o 1136 THR cc_start: 0.9008 (m) cc_final: 0.8770 (t) REVERT: o 1146 GLN cc_start: 0.8335 (pt0) cc_final: 0.7825 (pp30) REVERT: o 1282 ASP cc_start: 0.7773 (p0) cc_final: 0.7398 (p0) REVERT: o 1306 LYS cc_start: 0.7208 (mttt) cc_final: 0.6831 (mtpp) REVERT: o 1327 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7141 (tp30) REVERT: o 1351 ASP cc_start: 0.8072 (m-30) cc_final: 0.7814 (m-30) REVERT: o 1364 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6548 (mm-30) REVERT: o 1383 TYR cc_start: 0.7485 (t80) cc_final: 0.7099 (t80) REVERT: o 1396 ARG cc_start: 0.6890 (mtt-85) cc_final: 0.6374 (mtt-85) REVERT: o 1422 GLN cc_start: 0.6994 (mt0) cc_final: 0.6242 (mm110) REVERT: o 1478 GLU cc_start: 0.7371 (tt0) cc_final: 0.6819 (tp30) REVERT: o 1484 MET cc_start: 0.4096 (tmm) cc_final: 0.3669 (tmm) REVERT: p 141 GLN cc_start: 0.8537 (pt0) cc_final: 0.8228 (pm20) REVERT: p 143 GLN cc_start: 0.7413 (mp10) cc_final: 0.7159 (mp10) REVERT: p 144 HIS cc_start: 0.7515 (m-70) cc_final: 0.7182 (m170) REVERT: p 168 ASP cc_start: 0.6966 (p0) cc_final: 0.6638 (m-30) REVERT: p 169 ARG cc_start: 0.7415 (tmm-80) cc_final: 0.6826 (mmp80) REVERT: p 324 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7969 (mmm-85) REVERT: p 333 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6995 (tm-30) REVERT: p 341 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6444 (tm-30) REVERT: p 344 GLN cc_start: 0.7894 (mt0) cc_final: 0.7513 (tt0) REVERT: p 345 LYS cc_start: 0.7150 (mptt) cc_final: 0.6611 (mttp) REVERT: p 346 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6474 (mt-10) REVERT: p 388 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: p 528 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8101 (mt) REVERT: p 550 MET cc_start: 0.7335 (ttp) cc_final: 0.6911 (tmm) REVERT: p 606 ASP cc_start: 0.6509 (t0) cc_final: 0.6084 (t0) REVERT: p 630 LYS cc_start: 0.7807 (mttt) cc_final: 0.7574 (mmtm) REVERT: p 733 MET cc_start: 0.8291 (mtt) cc_final: 0.7947 (ttm) REVERT: p 828 VAL cc_start: 0.7556 (t) cc_final: 0.7325 (p) REVERT: p 863 ASP cc_start: 0.8104 (m-30) cc_final: 0.7311 (t0) REVERT: p 916 TYR cc_start: 0.5589 (m-10) cc_final: 0.5181 (m-80) REVERT: p 1022 LEU cc_start: 0.7512 (mt) cc_final: 0.7294 (tp) REVERT: p 1080 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7088 (mtp85) REVERT: p 1121 LEU cc_start: 0.7940 (mt) cc_final: 0.7602 (mt) REVERT: q 158 GLU cc_start: 0.7590 (tt0) cc_final: 0.7354 (pt0) REVERT: q 210 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8213 (mm-30) REVERT: s 44 PHE cc_start: 0.5902 (m-80) cc_final: 0.5674 (m-80) REVERT: s 72 MET cc_start: 0.8013 (ttt) cc_final: 0.7236 (ttp) REVERT: s 108 GLN cc_start: 0.8179 (mt0) cc_final: 0.7869 (mt0) REVERT: s 133 GLN cc_start: 0.8333 (mt0) cc_final: 0.7833 (mm-40) REVERT: s 154 GLU cc_start: 0.7176 (pm20) cc_final: 0.6764 (pm20) REVERT: s 159 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7787 (tp) REVERT: s 166 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6431 (mtm110) REVERT: t 79 VAL cc_start: 0.7270 (t) cc_final: 0.7052 (p) REVERT: t 115 TYR cc_start: 0.7994 (p90) cc_final: 0.7415 (p90) REVERT: v 4 ILE cc_start: 0.8558 (mt) cc_final: 0.8108 (mm) REVERT: v 37 MET cc_start: 0.7830 (mtp) cc_final: 0.7442 (mtt) REVERT: v 79 ASP cc_start: 0.6851 (m-30) cc_final: 0.6648 (t0) REVERT: v 95 LYS cc_start: 0.6872 (tttt) cc_final: 0.6280 (ttmm) REVERT: v 133 HIS cc_start: 0.7877 (m-70) cc_final: 0.7577 (m-70) REVERT: v 146 LYS cc_start: 0.7505 (tttt) cc_final: 0.6952 (ttpp) REVERT: w 15 ARG cc_start: 0.7849 (ptp90) cc_final: 0.6840 (ptp90) REVERT: w 29 ASP cc_start: 0.5892 (t0) cc_final: 0.5569 (t0) REVERT: w 63 ASP cc_start: 0.8738 (p0) cc_final: 0.8412 (p0) REVERT: w 71 ASP cc_start: 0.8682 (m-30) cc_final: 0.8447 (m-30) REVERT: w 93 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7751 (tt0) REVERT: x 48 MET cc_start: 0.8766 (mmp) cc_final: 0.8400 (mmt) REVERT: y 16 GLU cc_start: 0.7702 (tt0) cc_final: 0.7270 (tt0) REVERT: y 23 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7093 (tptt) REVERT: y 27 VAL cc_start: 0.8348 (t) cc_final: 0.7939 (m) REVERT: y 29 ASN cc_start: 0.7977 (m-40) cc_final: 0.7649 (m110) REVERT: y 82 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7142 (p) REVERT: z 25 GLU cc_start: 0.8314 (pm20) cc_final: 0.7965 (pm20) REVERT: z 35 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7280 (ttm170) outliers start: 109 outliers final: 91 residues processed: 589 average time/residue: 0.5108 time to fit residues: 481.7432 Evaluate side-chains 612 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 512 time to evaluate : 4.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 406 VAL Chi-restraints excluded: chain o residue 448 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 552 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 697 LYS Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1164 THR Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1270 GLN Chi-restraints excluded: chain o residue 1289 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1374 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 91 ILE Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 260 LEU Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 528 LEU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 602 SER Chi-restraints excluded: chain p residue 633 LEU Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 931 ILE Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain p residue 1075 MET Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain p residue 1133 HIS Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain s residue 197 SER Chi-restraints excluded: chain t residue 90 LEU Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 63 THR 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 113 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 23 LYS Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 82 SER Chi-restraints excluded: chain y residue 114 GLU Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 354 optimal weight: 1.9990 chunk 378 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 341 optimal weight: 0.0970 chunk 357 optimal weight: 1.9990 chunk 376 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36641 Z= 0.256 Angle : 0.463 10.125 49979 Z= 0.246 Chirality : 0.040 0.169 5567 Planarity : 0.003 0.060 6099 Dihedral : 16.239 109.291 5837 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 30.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.85 % Rotamer: Outliers : 3.01 % Allowed : 15.32 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.13), residues: 4137 helix: 2.18 (0.14), residues: 1379 sheet: 0.01 (0.19), residues: 684 loop : -0.20 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 479 HIS 0.024 0.001 HIS p1133 PHE 0.137 0.002 PHE o 431 TYR 0.016 0.001 TYR o 669 ARG 0.008 0.000 ARG o 430 *********************** 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 623 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 512 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: o 45 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: o 66 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8279 (mp0) REVERT: o 67 ARG cc_start: 0.8777 (ttp80) cc_final: 0.8487 (ttm110) REVERT: o 192 ARG cc_start: 0.7075 (ptt90) cc_final: 0.6759 (ptt90) REVERT: o 197 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7755 (mp0) REVERT: o 321 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6693 (mp0) REVERT: o 448 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7023 (ptt-90) REVERT: o 451 CYS cc_start: 0.6985 (m) cc_final: 0.6508 (p) REVERT: o 687 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8904 (tp) REVERT: o 700 GLN cc_start: 0.7600 (tt0) cc_final: 0.7368 (tp40) REVERT: o 712 ASP cc_start: 0.7144 (m-30) cc_final: 0.6741 (m-30) REVERT: o 803 LYS cc_start: 0.7609 (tttp) cc_final: 0.6996 (tptp) REVERT: o 824 GLU cc_start: 0.7956 (pt0) cc_final: 0.7671 (mp0) REVERT: o 953 GLU cc_start: 0.7881 (tp30) cc_final: 0.7426 (tp30) REVERT: o 1117 VAL cc_start: 0.6630 (t) cc_final: 0.6355 (p) REVERT: o 1128 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6413 (tt) REVERT: o 1132 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8401 (mmtm) REVERT: o 1136 THR cc_start: 0.9008 (m) cc_final: 0.8770 (t) REVERT: o 1146 GLN cc_start: 0.8355 (pt0) cc_final: 0.7841 (pp30) REVERT: o 1282 ASP cc_start: 0.7802 (p0) cc_final: 0.7443 (p0) REVERT: o 1303 GLN cc_start: 0.8202 (mt0) cc_final: 0.7620 (mp10) REVERT: o 1306 LYS cc_start: 0.7164 (mttt) cc_final: 0.6798 (mtpp) REVERT: o 1327 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: o 1351 ASP cc_start: 0.8076 (m-30) cc_final: 0.7815 (m-30) REVERT: o 1364 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6544 (mm-30) REVERT: o 1383 TYR cc_start: 0.7495 (t80) cc_final: 0.7117 (t80) REVERT: o 1396 ARG cc_start: 0.6791 (mtt-85) cc_final: 0.6312 (mtt-85) REVERT: o 1422 GLN cc_start: 0.6925 (mt0) cc_final: 0.6215 (mm-40) REVERT: o 1478 GLU cc_start: 0.7397 (tt0) cc_final: 0.6841 (tp30) REVERT: o 1484 MET cc_start: 0.4081 (tmm) cc_final: 0.3647 (tmm) REVERT: p 17 ILE cc_start: 0.8569 (mt) cc_final: 0.8243 (pt) REVERT: p 46 SER cc_start: 0.7320 (t) cc_final: 0.6959 (m) REVERT: p 141 GLN cc_start: 0.8545 (pt0) cc_final: 0.8230 (pm20) REVERT: p 143 GLN cc_start: 0.7422 (mp10) cc_final: 0.7165 (mp10) REVERT: p 144 HIS cc_start: 0.7505 (m-70) cc_final: 0.7157 (m170) REVERT: p 168 ASP cc_start: 0.6969 (p0) cc_final: 0.6646 (m-30) REVERT: p 169 ARG cc_start: 0.7419 (tmm-80) cc_final: 0.6831 (mmp80) REVERT: p 324 ARG cc_start: 0.8335 (mtt90) cc_final: 0.7956 (mmm-85) REVERT: p 333 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6999 (tm-30) REVERT: p 341 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6538 (tm-30) REVERT: p 344 GLN cc_start: 0.7916 (mt0) cc_final: 0.7537 (tt0) REVERT: p 345 LYS cc_start: 0.7162 (mptt) cc_final: 0.6642 (mttp) REVERT: p 346 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6452 (mt-10) REVERT: p 388 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7464 (m-80) REVERT: p 438 ARG cc_start: 0.6227 (mtm110) cc_final: 0.6001 (ttp-110) REVERT: p 550 MET cc_start: 0.7356 (ttp) cc_final: 0.6913 (tmm) REVERT: p 606 ASP cc_start: 0.6590 (t0) cc_final: 0.6189 (t0) REVERT: p 630 LYS cc_start: 0.7820 (mttt) cc_final: 0.7581 (mmtm) REVERT: p 733 MET cc_start: 0.8232 (mtt) cc_final: 0.7897 (ttm) REVERT: p 828 VAL cc_start: 0.7556 (t) cc_final: 0.7326 (p) REVERT: p 863 ASP cc_start: 0.8111 (m-30) cc_final: 0.7341 (t0) REVERT: p 916 TYR cc_start: 0.5627 (m-10) cc_final: 0.5222 (m-80) REVERT: p 1022 LEU cc_start: 0.7454 (mt) cc_final: 0.7244 (tp) REVERT: p 1080 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7162 (mtp85) REVERT: p 1121 LEU cc_start: 0.7963 (mt) cc_final: 0.7573 (mt) REVERT: q 158 GLU cc_start: 0.7596 (tt0) cc_final: 0.7359 (pt0) REVERT: q 210 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8223 (mm-30) REVERT: s 44 PHE cc_start: 0.5985 (m-80) cc_final: 0.5758 (m-80) REVERT: s 133 GLN cc_start: 0.8333 (mt0) cc_final: 0.7812 (mm-40) REVERT: s 154 GLU cc_start: 0.7186 (pm20) cc_final: 0.6774 (pm20) REVERT: s 159 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7800 (tp) REVERT: s 166 ARG cc_start: 0.7093 (mtt180) cc_final: 0.6419 (mtm110) REVERT: t 79 VAL cc_start: 0.7270 (t) cc_final: 0.7045 (p) REVERT: t 115 TYR cc_start: 0.7993 (p90) cc_final: 0.7402 (p90) REVERT: v 4 ILE cc_start: 0.8565 (mt) cc_final: 0.8108 (mm) REVERT: v 37 MET cc_start: 0.7854 (mtp) cc_final: 0.7471 (mtt) REVERT: v 95 LYS cc_start: 0.6862 (tttt) cc_final: 0.6290 (ttmm) REVERT: v 133 HIS cc_start: 0.7921 (m-70) cc_final: 0.7620 (m-70) REVERT: v 146 LYS cc_start: 0.7518 (tttt) cc_final: 0.7025 (ttpp) REVERT: w 15 ARG cc_start: 0.7853 (ptp90) cc_final: 0.6797 (ptp90) REVERT: w 29 ASP cc_start: 0.5933 (t0) cc_final: 0.5601 (t0) REVERT: w 50 ASN cc_start: 0.7089 (t0) cc_final: 0.6839 (t0) REVERT: w 71 ASP cc_start: 0.8780 (m-30) cc_final: 0.8549 (m-30) REVERT: w 93 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7908 (tt0) REVERT: x 48 MET cc_start: 0.8771 (mmp) cc_final: 0.8386 (mmt) REVERT: y 16 GLU cc_start: 0.7907 (tt0) cc_final: 0.7497 (tt0) REVERT: y 23 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7110 (tptt) REVERT: y 29 ASN cc_start: 0.8011 (m-40) cc_final: 0.7679 (m110) REVERT: y 82 SER cc_start: 0.7646 (OUTLIER) cc_final: 0.7142 (p) REVERT: z 25 GLU cc_start: 0.8324 (pm20) cc_final: 0.7975 (pm20) REVERT: z 35 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7272 (ttm170) outliers start: 111 outliers final: 93 residues processed: 587 average time/residue: 0.5568 time to fit residues: 525.0788 Evaluate side-chains 608 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 506 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 309 LEU Chi-restraints excluded: chain o residue 316 THR Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 406 VAL Chi-restraints excluded: chain o residue 448 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 552 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1027 ASP Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1135 LYS Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1289 GLU Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1374 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 235 ILE Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 524 LYS Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 602 SER Chi-restraints excluded: chain p residue 633 LEU Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 931 ILE Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1041 ILE Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 17 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain s residue 197 SER Chi-restraints excluded: chain t residue 102 ILE Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 63 THR 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 113 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain y residue 14 GLU Chi-restraints excluded: chain y residue 23 LYS Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 82 SER Chi-restraints excluded: chain y residue 114 GLU Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.0050 chunk 399 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 419 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 chunk 204 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1101 GLN p1133 HIS ** q 18 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** ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5720 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36641 Z= 0.170 Angle : 0.434 9.955 49979 Z= 0.233 Chirality : 0.039 0.166 5567 Planarity : 0.003 0.073 6099 Dihedral : 16.184 106.250 5837 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 2.63 % Allowed : 15.84 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.14), residues: 4137 helix: 2.33 (0.15), residues: 1386 sheet: 0.01 (0.19), residues: 702 loop : -0.14 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 679 HIS 0.004 0.001 HIS q 66 PHE 0.169 0.001 PHE o 431 TYR 0.013 0.001 TYR o 669 ARG 0.006 0.000 ARG o 334 ********************** 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 615 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 518 time to evaluate : 3.481 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 45 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: o 66 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8241 (mp0) REVERT: o 197 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7771 (mp0) REVERT: o 321 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6678 (mp0) REVERT: o 448 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.7039 (ptt-90) REVERT: o 451 CYS cc_start: 0.7001 (m) cc_final: 0.6507 (p) REVERT: o 687 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8864 (tp) REVERT: o 700 GLN cc_start: 0.7579 (tt0) cc_final: 0.7341 (tp-100) REVERT: o 712 ASP cc_start: 0.7120 (m-30) cc_final: 0.6711 (m-30) REVERT: o 803 LYS cc_start: 0.7627 (tttp) cc_final: 0.7011 (tptp) REVERT: o 824 GLU cc_start: 0.7951 (pt0) cc_final: 0.7675 (mp0) REVERT: o 868 MET cc_start: 0.7677 (ptt) cc_final: 0.7352 (ptm) REVERT: o 953 GLU cc_start: 0.7861 (tp30) cc_final: 0.7413 (tp30) REVERT: o 1117 VAL cc_start: 0.6607 (t) cc_final: 0.6388 (p) REVERT: o 1128 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6398 (tt) REVERT: o 1132 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8317 (mmtm) REVERT: o 1146 GLN cc_start: 0.8424 (pt0) cc_final: 0.7881 (pp30) REVERT: o 1282 ASP cc_start: 0.7777 (p0) cc_final: 0.7433 (p0) REVERT: o 1306 LYS cc_start: 0.7170 (mttt) cc_final: 0.6775 (mtpp) REVERT: o 1327 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: o 1351 ASP cc_start: 0.8074 (m-30) cc_final: 0.7815 (m-30) REVERT: o 1364 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6536 (mm-30) REVERT: o 1383 TYR cc_start: 0.7486 (t80) cc_final: 0.7116 (t80) REVERT: o 1396 ARG cc_start: 0.6888 (mtt-85) cc_final: 0.6428 (mtt-85) REVERT: o 1422 GLN cc_start: 0.6896 (mt0) cc_final: 0.6177 (mm110) REVERT: o 1478 GLU cc_start: 0.7400 (tt0) cc_final: 0.6833 (tp30) REVERT: o 1484 MET cc_start: 0.4093 (tmm) cc_final: 0.3668 (tmm) REVERT: p 17 ILE cc_start: 0.8623 (mt) cc_final: 0.8230 (pt) REVERT: p 141 GLN cc_start: 0.8803 (pt0) cc_final: 0.8443 (pm20) REVERT: p 143 GLN cc_start: 0.7422 (mp10) cc_final: 0.7169 (mp10) REVERT: p 144 HIS cc_start: 0.7515 (m-70) cc_final: 0.7174 (m170) REVERT: p 168 ASP cc_start: 0.6944 (p0) cc_final: 0.6646 (m-30) REVERT: p 169 ARG cc_start: 0.7408 (tmm-80) cc_final: 0.6828 (mmp80) REVERT: p 324 ARG cc_start: 0.8317 (mtt90) cc_final: 0.7967 (mmm-85) REVERT: p 333 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6985 (tm-30) REVERT: p 341 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6535 (tm-30) REVERT: p 344 GLN cc_start: 0.8051 (mt0) cc_final: 0.7679 (tt0) REVERT: p 345 LYS cc_start: 0.7148 (mptt) cc_final: 0.6641 (mttp) REVERT: p 346 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6442 (mt-10) REVERT: p 388 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: p 438 ARG cc_start: 0.6247 (mtm110) cc_final: 0.6034 (ttp-110) REVERT: p 550 MET cc_start: 0.7271 (ttp) cc_final: 0.6955 (tmm) REVERT: p 555 GLU cc_start: 0.7281 (mp0) cc_final: 0.7068 (mp0) REVERT: p 606 ASP cc_start: 0.6419 (t0) cc_final: 0.6043 (t0) REVERT: p 630 LYS cc_start: 0.7818 (mttt) cc_final: 0.7570 (mmtm) REVERT: p 733 MET cc_start: 0.8204 (mtt) cc_final: 0.7711 (ttm) REVERT: p 828 VAL cc_start: 0.7544 (t) cc_final: 0.7321 (p) REVERT: p 863 ASP cc_start: 0.8155 (m-30) cc_final: 0.7428 (t0) REVERT: p 916 TYR cc_start: 0.5543 (m-10) cc_final: 0.5158 (m-80) REVERT: p 1022 LEU cc_start: 0.7462 (mt) cc_final: 0.7249 (tp) REVERT: p 1080 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7227 (mtp85) REVERT: p 1121 LEU cc_start: 0.7960 (mt) cc_final: 0.7559 (mt) REVERT: q 158 GLU cc_start: 0.7511 (tt0) cc_final: 0.7307 (pt0) REVERT: q 210 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8217 (mm-30) REVERT: s 44 PHE cc_start: 0.5984 (m-80) cc_final: 0.5762 (m-80) REVERT: s 108 GLN cc_start: 0.8106 (mt0) cc_final: 0.7839 (mt0) REVERT: s 133 GLN cc_start: 0.8324 (mt0) cc_final: 0.7798 (mm-40) REVERT: s 154 GLU cc_start: 0.7170 (pm20) cc_final: 0.6756 (pm20) REVERT: s 159 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7775 (tp) REVERT: s 166 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6484 (mtm110) REVERT: t 79 VAL cc_start: 0.7258 (t) cc_final: 0.7043 (p) REVERT: t 115 TYR cc_start: 0.8000 (p90) cc_final: 0.7410 (p90) REVERT: u 164 MET cc_start: 0.2658 (mtt) cc_final: 0.2049 (mmt) REVERT: v 4 ILE cc_start: 0.8574 (mt) cc_final: 0.8113 (mm) REVERT: v 37 MET cc_start: 0.7789 (mtp) cc_final: 0.7408 (mtt) REVERT: v 95 LYS cc_start: 0.6828 (tttt) cc_final: 0.6250 (ttmm) REVERT: v 99 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7920 (mm) REVERT: v 146 LYS cc_start: 0.7508 (tttt) cc_final: 0.6963 (ttpp) REVERT: w 15 ARG cc_start: 0.7851 (ptp90) cc_final: 0.6766 (ptp90) REVERT: w 29 ASP cc_start: 0.5884 (t0) cc_final: 0.5553 (t0) REVERT: w 71 ASP cc_start: 0.8805 (m-30) cc_final: 0.8565 (m-30) REVERT: w 93 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7835 (tt0) REVERT: x 48 MET cc_start: 0.8764 (mmp) cc_final: 0.8407 (mmt) REVERT: x 58 LYS cc_start: 0.8270 (mmmm) cc_final: 0.7913 (mmtp) REVERT: y 16 GLU cc_start: 0.7579 (tt0) cc_final: 0.7158 (tt0) REVERT: y 23 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7024 (tptt) REVERT: y 29 ASN cc_start: 0.8005 (m-40) cc_final: 0.7458 (m-40) REVERT: y 82 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7165 (p) REVERT: z 42 ARG cc_start: 0.8376 (mtp180) cc_final: 0.8056 (mmm-85) outliers start: 97 outliers final: 85 residues processed: 587 average time/residue: 0.5181 time to fit residues: 484.8786 Evaluate side-chains 606 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 511 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 110 VAL Chi-restraints excluded: chain o residue 286 ILE Chi-restraints excluded: chain o residue 301 HIS Chi-restraints excluded: chain o residue 375 ILE Chi-restraints excluded: chain o residue 395 THR Chi-restraints excluded: chain o residue 406 VAL Chi-restraints excluded: chain o residue 448 ARG Chi-restraints excluded: chain o residue 488 VAL Chi-restraints excluded: chain o residue 490 THR Chi-restraints excluded: chain o residue 552 ASP Chi-restraints excluded: chain o residue 659 GLU Chi-restraints excluded: chain o residue 687 ILE Chi-restraints excluded: chain o residue 689 ILE Chi-restraints excluded: chain o residue 695 ASP Chi-restraints excluded: chain o residue 849 ASP Chi-restraints excluded: chain o residue 872 MET Chi-restraints excluded: chain o residue 909 LEU Chi-restraints excluded: chain o residue 934 LEU Chi-restraints excluded: chain o residue 1027 ASP Chi-restraints excluded: chain o residue 1118 THR Chi-restraints excluded: chain o residue 1128 ILE Chi-restraints excluded: chain o residue 1133 LYS Chi-restraints excluded: chain o residue 1138 SER Chi-restraints excluded: chain o residue 1165 THR Chi-restraints excluded: chain o residue 1211 LEU Chi-restraints excluded: chain o residue 1214 VAL Chi-restraints excluded: chain o residue 1327 GLU Chi-restraints excluded: chain o residue 1338 THR Chi-restraints excluded: chain o residue 1374 VAL Chi-restraints excluded: chain o residue 1389 ASP Chi-restraints excluded: chain o residue 1411 LEU Chi-restraints excluded: chain o residue 1430 CYS Chi-restraints excluded: chain p residue 36 GLU Chi-restraints excluded: chain p residue 93 LEU Chi-restraints excluded: chain p residue 203 ASN Chi-restraints excluded: chain p residue 260 LEU Chi-restraints excluded: chain p residue 272 VAL Chi-restraints excluded: chain p residue 342 VAL Chi-restraints excluded: chain p residue 351 VAL Chi-restraints excluded: chain p residue 381 GLU Chi-restraints excluded: chain p residue 388 TYR Chi-restraints excluded: chain p residue 447 SER Chi-restraints excluded: chain p residue 450 THR Chi-restraints excluded: chain p residue 471 ASN Chi-restraints excluded: chain p residue 485 LEU Chi-restraints excluded: chain p residue 570 ASN Chi-restraints excluded: chain p residue 602 SER Chi-restraints excluded: chain p residue 633 LEU Chi-restraints excluded: chain p residue 719 SER Chi-restraints excluded: chain p residue 809 VAL Chi-restraints excluded: chain p residue 866 ILE Chi-restraints excluded: chain p residue 921 ILE Chi-restraints excluded: chain p residue 931 ILE Chi-restraints excluded: chain p residue 952 GLU Chi-restraints excluded: chain p residue 1007 ASN Chi-restraints excluded: chain p residue 1054 MET Chi-restraints excluded: chain p residue 1084 LEU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 16 ASP Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain q residue 75 SER Chi-restraints excluded: chain q residue 85 SER Chi-restraints excluded: chain q residue 94 CYS Chi-restraints excluded: chain q residue 212 ASP Chi-restraints excluded: chain r residue 43 HIS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 82 VAL Chi-restraints excluded: chain s residue 104 ILE Chi-restraints excluded: chain s residue 159 LEU Chi-restraints excluded: chain s residue 168 ASN Chi-restraints excluded: chain s residue 185 ILE Chi-restraints excluded: chain s residue 197 SER Chi-restraints excluded: chain u residue 45 VAL Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 111 HIS Chi-restraints excluded: chain v residue 38 ASP Chi-restraints excluded: chain v residue 47 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 51 ASP Chi-restraints excluded: chain v residue 63 THR Chi-restraints excluded: chain v residue 87 GLN Chi-restraints excluded: chain v residue 99 ILE Chi-restraints excluded: chain v residue 113 SER Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 77 THR Chi-restraints excluded: chain w residue 124 THR Chi-restraints excluded: chain y residue 23 LYS Chi-restraints excluded: chain y residue 42 LEU Chi-restraints excluded: chain y residue 82 SER Chi-restraints excluded: chain y residue 114 GLU Chi-restraints excluded: chain z residue 28 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 343 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** o 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 449 HIS ** o 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p1133 HIS ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 107 GLN ** t 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 126 GLN ** w 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 23 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.167077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109897 restraints weight = 47860.239| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.21 r_work: 0.2997 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 36641 Z= 0.546 Angle : 0.621 10.669 49979 Z= 0.324 Chirality : 0.045 0.187 5567 Planarity : 0.005 0.061 6099 Dihedral : 16.289 102.103 5837 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.88 % Rotamer: Outliers : 3.09 % Allowed : 15.40 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.13), residues: 4137 helix: 1.54 (0.14), residues: 1385 sheet: -0.22 (0.19), residues: 706 loop : -0.43 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP q 49 HIS 0.007 0.002 HIS o1108 PHE 0.133 0.003 PHE o 431 TYR 0.024 0.002 TYR o 669 ARG 0.008 0.001 ARG q 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10535.60 seconds wall clock time: 189 minutes 8.58 seconds (11348.58 seconds total)