Starting phenix.real_space_refine on Wed Mar 20 07:52:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g00_29640/03_2024/8g00_29640.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g00_29640/03_2024/8g00_29640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g00_29640/03_2024/8g00_29640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g00_29640/03_2024/8g00_29640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g00_29640/03_2024/8g00_29640.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g00_29640/03_2024/8g00_29640.pdb" } resolution = 3.4 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= 0.002 sd= 0.078 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: 6 Type Number sf(0) Gaussians P 94 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16490 2.51 5 N 4752 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 29": "OE1" <-> "OE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H ASP 197": "OD1" <-> "OD2" Residue "I ASP 42": "OD1" <-> "OD2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 264": "OD1" <-> "OD2" Residue "J GLU 402": "OE1" <-> "OE2" 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: 26819 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Inner-chain residues flagged as termini: ['pdbres=" DG A 25 "'] Classifications: {'DNA': 19} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 631 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "G" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1702 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10381 Classifications: {'peptide': 1316} Link IDs: {'PTRANS': 55, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 10403 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 55, 'TRANS': 1281} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 997 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 11, 'rna3p': 35} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.17, per 1000 atoms: 0.53 Number of scatterers: 26819 At special positions: 0 Unit cell: (138, 159, 163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 94 15.00 Mg 1 11.99 O 5376 8.00 N 4752 7.00 C 16490 6.00 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=0, symmetry=0 Time building additional restraints: 11.50 Conformation dependent library (CDL) restraints added in 4.4 seconds 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 45 sheets defined 38.7% alpha, 13.8% beta 32 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 8.79 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 88 removed outlier: 3.502A pdb=" N LEU G 88 " --> pdb=" O ASN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 158 removed outlier: 4.116A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 229 Processing helix chain 'H' and resid 34 through 49 removed outlier: 3.514A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.561A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 158 Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'H' and resid 228 through 232 removed outlier: 4.128A pdb=" N VAL H 232 " --> pdb=" O GLU H 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.685A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.880A pdb=" N SER I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 4.182A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.930A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 Processing helix chain 'I' and resid 270 through 281 Processing helix chain 'I' and resid 291 through 295 Processing helix chain 'I' and resid 318 through 329 Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.618A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 508 removed outlier: 4.643A pdb=" N ILE I 498 " --> pdb=" O ASN I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 544 through 549 removed outlier: 3.525A pdb=" N ARG I 548 " --> pdb=" O GLY I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.757A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 612 removed outlier: 4.010A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 662 through 667 removed outlier: 3.572A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.655A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 removed outlier: 3.849A pdb=" N MET I 741 " --> pdb=" O GLU I 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 738 through 741' Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 865 removed outlier: 3.541A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU I 865 " --> pdb=" O ALA I 861 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.739A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 4.167A pdb=" N GLU I1026 " --> pdb=" O LYS I1022 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS I1027 " --> pdb=" O HIS I1023 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1099 through 1103 Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.667A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 3.637A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 removed outlier: 3.538A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.619A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.821A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1285 through 1292 Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1334 removed outlier: 3.718A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY I1334 " --> pdb=" O ILE I1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 removed outlier: 3.849A pdb=" N GLU J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 208 removed outlier: 4.402A pdb=" N GLU J 203 " --> pdb=" O GLU J 199 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.659A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 264 through 286 Processing helix chain 'J' and resid 288 through 309 Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.547A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 452 through 458 removed outlier: 4.386A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.768A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.567A pdb=" N TRP J 580 " --> pdb=" O ARG J 576 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 removed outlier: 3.669A pdb=" N ILE J 591 " --> pdb=" O PRO J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 597 through 612 Processing helix chain 'J' and resid 614 through 636 Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.499A pdb=" N LEU J 740 " --> pdb=" O GLN J 736 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA J 741 " --> pdb=" O ILE J 737 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.810A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 865 through 875 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 915 through 925 Processing helix chain 'J' and resid 926 through 930 Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.114A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.128A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.998A pdb=" N ASN J1295 " --> pdb=" O GLU J1291 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1313 Processing helix chain 'J' and resid 1318 through 1326 removed outlier: 3.673A pdb=" N SER J1324 " --> pdb=" O ILE J1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1339 Processing helix chain 'J' and resid 1346 through 1354 Processing helix chain 'J' and resid 1360 through 1372 removed outlier: 4.128A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.936A pdb=" N LEU K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 77 Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 9.100A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.366A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.507A pdb=" N ARG G 91 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.593A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 180 through 182 removed outlier: 6.584A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 23 through 27 removed outlier: 6.543A pdb=" N LEU H 198 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA H 189 " --> pdb=" O LEU H 198 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS H 200 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL H 187 " --> pdb=" O LYS H 200 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL H 202 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR H 185 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.590A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL H 146 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN H 147 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA H 55 " --> pdb=" O GLN H 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AB1, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.837A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB4, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.533A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 66 through 75 removed outlier: 5.652A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET I 124 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB7, first strand: chain 'I' and resid 451 through 454 Processing sheet with id=AB8, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.636A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AC1, first strand: chain 'I' and resid 239 through 240 removed outlier: 3.509A pdb=" N MET I 239 " --> pdb=" O ILE I 285 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.790A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 301 through 302 removed outlier: 3.564A pdb=" N CYS I 311 " --> pdb=" O TYR I 301 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.540A pdb=" N GLN I 580 " --> pdb=" O GLU I 588 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 599 through 603 removed outlier: 5.551A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.740A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'I' and resid 1065 through 1067 removed outlier: 7.931A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 830 through 841 removed outlier: 3.798A pdb=" N LYS I1048 " --> pdb=" O SER I 840 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LYS I1057 " --> pdb=" O GLY I 926 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLY I 926 " --> pdb=" O LYS I1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.264A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD4, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.528A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AD8, first strand: chain 'J' and resid 350 through 356 removed outlier: 6.420A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER J 353 " --> pdb=" O MET J 466 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 547 through 556 removed outlier: 3.613A pdb=" N VAL J 550 " --> pdb=" O LYS J 570 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 809 through 811 removed outlier: 6.194A pdb=" N VAL J 894 " --> pdb=" O VAL J 809 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU J 811 " --> pdb=" O VAL J 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'J' and resid 825 through 826 removed outlier: 7.269A pdb=" N VAL J 825 " --> pdb=" O LYS J 832 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS J 832 " --> pdb=" O VAL J 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 949 through 951 Processing sheet with id=AE5, first strand: chain 'J' and resid 957 through 960 removed outlier: 3.641A pdb=" N LYS J 959 " --> pdb=" O LYS J 983 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS J 983 " --> pdb=" O LYS J 959 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1034 through 1036 removed outlier: 3.531A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1059 through 1061 removed outlier: 3.593A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AE9, first strand: chain 'J' and resid 1279 through 1281 996 hydrogen bonds defined for protein. 2781 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 12.45 Time building geometry restraints manager: 12.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7164 1.33 - 1.45: 4628 1.45 - 1.57: 15259 1.57 - 1.69: 187 1.69 - 1.81: 184 Bond restraints: 27422 Sorted by residual: bond pdb=" N VAL G 232 " pdb=" CA VAL G 232 " ideal model delta sigma weight residual 1.458 1.498 -0.039 1.17e-02 7.31e+03 1.14e+01 bond pdb=" N GLY I 48 " pdb=" CA GLY I 48 " ideal model delta sigma weight residual 1.448 1.478 -0.030 9.20e-03 1.18e+04 1.09e+01 bond pdb=" N LEU G 31 " pdb=" CA LEU G 31 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.25e-02 6.40e+03 1.06e+01 bond pdb=" N ILE J 147 " pdb=" CA ILE J 147 " ideal model delta sigma weight residual 1.457 1.495 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N LEU J 120 " pdb=" CA LEU J 120 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.03e+01 ... (remaining 27417 not shown) Histogram of bond angle deviations from ideal: 96.23 - 103.80: 573 103.80 - 111.37: 12148 111.37 - 118.95: 10648 118.95 - 126.52: 13600 126.52 - 134.09: 506 Bond angle restraints: 37475 Sorted by residual: angle pdb=" N TYR J 46 " pdb=" CA TYR J 46 " pdb=" C TYR J 46 " ideal model delta sigma weight residual 112.90 105.37 7.53 1.31e+00 5.83e-01 3.30e+01 angle pdb=" C ASP J 54 " pdb=" N GLY J 55 " pdb=" CA GLY J 55 " ideal model delta sigma weight residual 122.77 116.56 6.21 1.21e+00 6.83e-01 2.63e+01 angle pdb=" C ARG J 250 " pdb=" CA ARG J 250 " pdb=" CB ARG J 250 " ideal model delta sigma weight residual 111.29 120.33 -9.04 1.92e+00 2.71e-01 2.21e+01 angle pdb=" N LEU I1291 " pdb=" CA LEU I1291 " pdb=" C LEU I1291 " ideal model delta sigma weight residual 113.61 106.59 7.02 1.50e+00 4.44e-01 2.19e+01 angle pdb=" N PRO G 30 " pdb=" CA PRO G 30 " pdb=" C PRO G 30 " ideal model delta sigma weight residual 110.74 118.35 -7.61 1.66e+00 3.63e-01 2.10e+01 ... (remaining 37470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 16058 35.89 - 71.78: 635 71.78 - 107.67: 43 107.67 - 143.56: 4 143.56 - 179.45: 3 Dihedral angle restraints: 16743 sinusoidal: 7640 harmonic: 9103 Sorted by residual: dihedral pdb=" O4' C R 17 " pdb=" C1' C R 17 " pdb=" N1 C R 17 " pdb=" C2 C R 17 " ideal model delta sinusoidal sigma weight residual 200.00 56.43 143.57 1 1.50e+01 4.44e-03 7.70e+01 dihedral pdb=" O4' U R 15 " pdb=" C1' U R 15 " pdb=" N1 U R 15 " pdb=" C2 U R 15 " ideal model delta sinusoidal sigma weight residual 200.00 57.75 142.25 1 1.50e+01 4.44e-03 7.64e+01 dihedral pdb=" O4' G R 38 " pdb=" C2' G R 38 " pdb=" C1' G R 38 " pdb=" C3' G R 38 " ideal model delta sinusoidal sigma weight residual 25.00 -15.28 40.28 1 8.00e+00 1.56e-02 3.56e+01 ... (remaining 16740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3859 0.079 - 0.158: 412 0.158 - 0.237: 37 0.237 - 0.316: 6 0.316 - 0.394: 3 Chirality restraints: 4317 Sorted by residual: chirality pdb=" CG LEU J 194 " pdb=" CB LEU J 194 " pdb=" CD1 LEU J 194 " pdb=" CD2 LEU J 194 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CG LEU I1278 " pdb=" CB LEU I1278 " pdb=" CD1 LEU I1278 " pdb=" CD2 LEU I1278 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CG LEU J1314 " pdb=" CB LEU J1314 " pdb=" CD1 LEU J1314 " pdb=" CD2 LEU J1314 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 4314 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 36 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLN I 36 " -0.077 2.00e-02 2.50e+03 pdb=" O GLN I 36 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS I 37 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 44 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ILE J 44 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE J 44 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN J 45 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 802 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.80e+00 pdb=" CG ASP J 802 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP J 802 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP J 802 " 0.018 2.00e-02 2.50e+03 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 307 2.60 - 3.18: 23130 3.18 - 3.75: 43758 3.75 - 4.33: 59048 4.33 - 4.90: 96572 Nonbonded interactions: 222815 Sorted by model distance: nonbonded pdb=" OD1 ASN I1108 " pdb=" NE2 GLN I1111 " model vdw 2.029 2.520 nonbonded pdb=" CB ASP J 460 " pdb="MG MG J1501 " model vdw 2.103 2.570 nonbonded pdb=" O ARG G 45 " pdb=" OG SER G 49 " model vdw 2.196 2.440 nonbonded pdb=" OD2 ASP I 160 " pdb=" OG1 THR I 164 " model vdw 2.207 2.440 nonbonded pdb=" O2' G R 6 " pdb=" O2' A R 27 " model vdw 2.208 2.440 ... (remaining 222810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 234)) selection = (chain 'H' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 234)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.150 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 78.580 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.004 0.072 27422 Z= 0.270 Angle : 0.665 9.583 37475 Z= 0.392 Chirality : 0.049 0.394 4317 Planarity : 0.004 0.093 4556 Dihedral : 17.679 179.451 10887 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 1.41 % Allowed : 1.11 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.15), residues: 3152 helix: 1.21 (0.16), residues: 1081 sheet: -0.35 (0.29), residues: 322 loop : -0.66 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 580 HIS 0.002 0.000 HIS J 430 PHE 0.048 0.001 PHE I1265 TYR 0.026 0.001 TYR J 144 ARG 0.016 0.000 ARG J 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 478 time to evaluate : 2.745 Fit side-chains revert: symmetry clash REVERT: G 176 CYS cc_start: 0.7265 (t) cc_final: 0.7051 (p) REVERT: H 71 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8577 (mtmt) REVERT: H 185 TYR cc_start: 0.8282 (p90) cc_final: 0.8009 (p90) REVERT: H 192 VAL cc_start: 0.6342 (OUTLIER) cc_final: 0.6141 (p) REVERT: I 47 TYR cc_start: 0.3409 (m-10) cc_final: 0.2277 (m-10) REVERT: I 496 LYS cc_start: 0.8126 (tttt) cc_final: 0.7535 (mppt) REVERT: I 1080 ASN cc_start: 0.8693 (t0) cc_final: 0.8382 (t0) REVERT: J 136 GLU cc_start: 0.8187 (pp20) cc_final: 0.6834 (tp30) REVERT: J 140 TYR cc_start: 0.7601 (m-10) cc_final: 0.6706 (m-10) REVERT: J 440 VAL cc_start: 0.9285 (t) cc_final: 0.9081 (p) REVERT: J 458 ASN cc_start: 0.8488 (t0) cc_final: 0.8271 (t0) REVERT: J 698 MET cc_start: 0.8625 (mmm) cc_final: 0.8362 (mmm) REVERT: J 992 LYS cc_start: 0.8489 (mmmt) cc_final: 0.7774 (mtpp) REVERT: J 1349 GLU cc_start: 0.7683 (mp0) cc_final: 0.7441 (mp0) REVERT: K 11 GLU cc_start: 0.7399 (mp0) cc_final: 0.7119 (mp0) REVERT: K 71 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7731 (mm-30) outliers start: 38 outliers final: 4 residues processed: 495 average time/residue: 0.4387 time to fit residues: 328.2531 Evaluate side-chains 320 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 315 time to evaluate : 2.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 120 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 252 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27422 Z= 0.288 Angle : 0.599 10.611 37475 Z= 0.310 Chirality : 0.043 0.190 4317 Planarity : 0.004 0.050 4556 Dihedral : 15.865 179.706 4700 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.92 % Favored : 95.05 % Rotamer: Outliers : 1.67 % Allowed : 12.75 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.15), residues: 3152 helix: 1.18 (0.16), residues: 1108 sheet: -0.76 (0.27), residues: 351 loop : -0.70 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 580 HIS 0.005 0.001 HIS J 545 PHE 0.032 0.002 PHE I1025 TYR 0.029 0.001 TYR H 177 ARG 0.009 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 352 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 141 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8475 (p) REVERT: G 176 CYS cc_start: 0.7510 (t) cc_final: 0.7052 (p) REVERT: H 62 ASP cc_start: 0.6618 (p0) cc_final: 0.6171 (p0) REVERT: H 93 GLN cc_start: 0.5928 (mp10) cc_final: 0.4640 (mp10) REVERT: H 185 TYR cc_start: 0.8514 (p90) cc_final: 0.8143 (p90) REVERT: H 197 ASP cc_start: 0.6578 (p0) cc_final: 0.6355 (p0) REVERT: I 47 TYR cc_start: 0.2827 (m-10) cc_final: 0.2203 (m-10) REVERT: I 142 GLU cc_start: 0.7717 (tt0) cc_final: 0.7505 (tp30) REVERT: I 443 ASP cc_start: 0.7819 (p0) cc_final: 0.7535 (p0) REVERT: I 496 LYS cc_start: 0.8224 (tttt) cc_final: 0.7616 (mppt) REVERT: I 1034 ARG cc_start: 0.8199 (mmp80) cc_final: 0.7998 (mmp80) REVERT: J 52 GLU cc_start: 0.7122 (tp30) cc_final: 0.6645 (mm-30) REVERT: J 96 LYS cc_start: 0.8443 (ptpt) cc_final: 0.8220 (pptt) REVERT: J 136 GLU cc_start: 0.8073 (pp20) cc_final: 0.7202 (tp30) REVERT: J 140 TYR cc_start: 0.7749 (m-10) cc_final: 0.6963 (m-10) REVERT: J 186 GLN cc_start: 0.8111 (tt0) cc_final: 0.7859 (tt0) REVERT: J 307 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7838 (mp) REVERT: J 440 VAL cc_start: 0.9240 (t) cc_final: 0.9013 (p) REVERT: J 478 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8586 (tp) REVERT: J 625 MET cc_start: 0.8591 (ttp) cc_final: 0.8191 (ttp) REVERT: J 847 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: J 992 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7666 (mtpp) REVERT: J 1174 ARG cc_start: 0.8291 (ptt-90) cc_final: 0.7964 (ttp80) REVERT: J 1195 GLN cc_start: 0.6933 (mt0) cc_final: 0.6600 (mp10) REVERT: K 11 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7333 (mp0) outliers start: 45 outliers final: 26 residues processed: 378 average time/residue: 0.4028 time to fit residues: 242.8901 Evaluate side-chains 328 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 297 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 0.0970 chunk 90 optimal weight: 0.6980 chunk 243 optimal weight: 9.9990 chunk 199 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 292 optimal weight: 0.0050 chunk 316 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 488 ASN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 736 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27422 Z= 0.170 Angle : 0.530 9.628 37475 Z= 0.273 Chirality : 0.041 0.203 4317 Planarity : 0.004 0.045 4556 Dihedral : 15.730 177.651 4695 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.78 % Allowed : 16.23 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.15), residues: 3152 helix: 1.35 (0.16), residues: 1114 sheet: -0.72 (0.27), residues: 351 loop : -0.66 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 115 HIS 0.004 0.001 HIS H 37 PHE 0.036 0.001 PHE I1025 TYR 0.017 0.001 TYR H 177 ARG 0.006 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 345 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 141 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8559 (p) REVERT: G 176 CYS cc_start: 0.7458 (t) cc_final: 0.7070 (p) REVERT: H 147 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: H 185 TYR cc_start: 0.8483 (p90) cc_final: 0.8135 (p90) REVERT: H 197 ASP cc_start: 0.6810 (p0) cc_final: 0.6582 (p0) REVERT: I 47 TYR cc_start: 0.2833 (m-10) cc_final: 0.2197 (m-10) REVERT: I 237 LEU cc_start: 0.6984 (tt) cc_final: 0.6717 (mp) REVERT: I 364 VAL cc_start: 0.8901 (m) cc_final: 0.8588 (p) REVERT: I 443 ASP cc_start: 0.7740 (p0) cc_final: 0.7382 (p0) REVERT: I 496 LYS cc_start: 0.8169 (tttt) cc_final: 0.7595 (mppt) REVERT: I 798 GLN cc_start: 0.7964 (tt0) cc_final: 0.7553 (mt0) REVERT: I 1034 ARG cc_start: 0.8260 (mmp80) cc_final: 0.8032 (mmp80) REVERT: I 1233 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8720 (mt) REVERT: I 1279 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7644 (mt-10) REVERT: J 52 GLU cc_start: 0.7096 (tp30) cc_final: 0.6711 (mm-30) REVERT: J 96 LYS cc_start: 0.8361 (ptpt) cc_final: 0.8085 (pptt) REVERT: J 136 GLU cc_start: 0.8033 (pp20) cc_final: 0.7420 (tp30) REVERT: J 140 TYR cc_start: 0.7870 (m-10) cc_final: 0.6873 (m-10) REVERT: J 144 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: J 343 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8479 (mm) REVERT: J 375 GLU cc_start: 0.8031 (tp30) cc_final: 0.7746 (tp30) REVERT: J 625 MET cc_start: 0.8471 (ttp) cc_final: 0.8205 (ttp) REVERT: J 698 MET cc_start: 0.8768 (mmm) cc_final: 0.8457 (mmm) REVERT: J 847 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: J 992 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7670 (mtpp) REVERT: J 1174 ARG cc_start: 0.8363 (ptt-90) cc_final: 0.8009 (ttp80) REVERT: J 1195 GLN cc_start: 0.6887 (mt0) cc_final: 0.6567 (mp10) REVERT: J 1197 ASN cc_start: 0.7613 (p0) cc_final: 0.6515 (t0) REVERT: K 11 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: K 63 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7713 (mp) REVERT: K 70 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7578 (mm-40) outliers start: 48 outliers final: 30 residues processed: 377 average time/residue: 0.3929 time to fit residues: 231.7132 Evaluate side-chains 343 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 305 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 717 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 144 TYR Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 293 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 278 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27422 Z= 0.251 Angle : 0.547 8.951 37475 Z= 0.282 Chirality : 0.042 0.198 4317 Planarity : 0.004 0.044 4556 Dihedral : 15.739 177.530 4693 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.74 % Allowed : 18.12 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.15), residues: 3152 helix: 1.33 (0.16), residues: 1109 sheet: -0.76 (0.28), residues: 341 loop : -0.65 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 115 HIS 0.004 0.001 HIS J 430 PHE 0.026 0.002 PHE I1025 TYR 0.019 0.001 TYR I1229 ARG 0.007 0.000 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 323 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 141 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8533 (p) REVERT: G 176 CYS cc_start: 0.7535 (t) cc_final: 0.7032 (p) REVERT: H 147 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: H 185 TYR cc_start: 0.8618 (p90) cc_final: 0.8215 (p90) REVERT: I 47 TYR cc_start: 0.3012 (m-10) cc_final: 0.2095 (m-10) REVERT: I 97 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7555 (mmt180) REVERT: I 237 LEU cc_start: 0.7010 (tt) cc_final: 0.6729 (mp) REVERT: I 443 ASP cc_start: 0.7845 (p0) cc_final: 0.7427 (p0) REVERT: I 496 LYS cc_start: 0.8209 (tttt) cc_final: 0.7611 (mppt) REVERT: I 1034 ARG cc_start: 0.8263 (mmp80) cc_final: 0.8010 (mmp80) REVERT: I 1233 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8705 (mt) REVERT: I 1279 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7795 (mt-10) REVERT: J 52 GLU cc_start: 0.7075 (tp30) cc_final: 0.6812 (mm-30) REVERT: J 96 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8161 (pptt) REVERT: J 136 GLU cc_start: 0.7992 (pp20) cc_final: 0.7436 (tp30) REVERT: J 140 TYR cc_start: 0.7935 (m-10) cc_final: 0.7074 (m-10) REVERT: J 180 MET cc_start: 0.8094 (tmm) cc_final: 0.7845 (tmm) REVERT: J 237 MET cc_start: 0.8827 (mtt) cc_final: 0.8524 (mtt) REVERT: J 239 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8576 (pp) REVERT: J 307 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7950 (mp) REVERT: J 375 GLU cc_start: 0.8272 (tp30) cc_final: 0.7952 (tp30) REVERT: J 457 TYR cc_start: 0.8578 (m-80) cc_final: 0.8249 (m-80) REVERT: J 847 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: J 992 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7949 (mtpp) REVERT: J 1174 ARG cc_start: 0.8412 (ptt-90) cc_final: 0.8188 (ttp80) REVERT: J 1195 GLN cc_start: 0.7078 (mt0) cc_final: 0.6782 (mp10) REVERT: J 1349 GLU cc_start: 0.7527 (mp0) cc_final: 0.7254 (mp0) REVERT: K 11 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7253 (mp0) outliers start: 74 outliers final: 44 residues processed: 379 average time/residue: 0.3943 time to fit residues: 238.5527 Evaluate side-chains 349 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 297 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 97 ARG Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 843 THR Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 955 LYS Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 0.0060 chunk 176 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 279 optimal weight: 0.0470 chunk 78 optimal weight: 30.0000 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27422 Z= 0.146 Angle : 0.511 9.178 37475 Z= 0.263 Chirality : 0.040 0.205 4317 Planarity : 0.003 0.046 4556 Dihedral : 15.672 176.001 4693 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.70 % Allowed : 19.41 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.15), residues: 3152 helix: 1.54 (0.16), residues: 1092 sheet: -0.52 (0.29), residues: 321 loop : -0.58 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 115 HIS 0.003 0.001 HIS H 37 PHE 0.031 0.001 PHE G 35 TYR 0.016 0.001 TYR I1229 ARG 0.006 0.000 ARG I 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 347 time to evaluate : 2.781 Fit side-chains revert: symmetry clash REVERT: G 141 SER cc_start: 0.8774 (m) cc_final: 0.8555 (p) REVERT: G 176 CYS cc_start: 0.7446 (t) cc_final: 0.7096 (p) REVERT: H 84 ASN cc_start: 0.8071 (m110) cc_final: 0.7669 (m110) REVERT: H 147 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: H 185 TYR cc_start: 0.8497 (p90) cc_final: 0.8144 (p90) REVERT: H 197 ASP cc_start: 0.6609 (p0) cc_final: 0.6384 (p0) REVERT: I 47 TYR cc_start: 0.2869 (m-10) cc_final: 0.1748 (m-80) REVERT: I 97 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7584 (mmt180) REVERT: I 423 ASP cc_start: 0.7948 (p0) cc_final: 0.7708 (p0) REVERT: I 443 ASP cc_start: 0.7650 (p0) cc_final: 0.7355 (p0) REVERT: I 496 LYS cc_start: 0.8186 (tttt) cc_final: 0.7577 (mppt) REVERT: I 1233 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8649 (mt) REVERT: J 52 GLU cc_start: 0.6879 (tp30) cc_final: 0.6670 (mm-30) REVERT: J 53 ARG cc_start: 0.8222 (tmt170) cc_final: 0.7971 (tpt90) REVERT: J 96 LYS cc_start: 0.8306 (ptpt) cc_final: 0.8048 (pptt) REVERT: J 129 ASP cc_start: 0.7313 (t0) cc_final: 0.6730 (t0) REVERT: J 136 GLU cc_start: 0.7830 (pp20) cc_final: 0.7383 (tp30) REVERT: J 140 TYR cc_start: 0.7742 (m-10) cc_final: 0.6878 (m-10) REVERT: J 180 MET cc_start: 0.8142 (tmm) cc_final: 0.7860 (tmm) REVERT: J 186 GLN cc_start: 0.7687 (tt0) cc_final: 0.7138 (tt0) REVERT: J 237 MET cc_start: 0.8851 (mtt) cc_final: 0.8562 (mtt) REVERT: J 312 ARG cc_start: 0.6084 (mmm160) cc_final: 0.5873 (mmm160) REVERT: J 375 GLU cc_start: 0.8179 (tp30) cc_final: 0.7909 (tp30) REVERT: J 698 MET cc_start: 0.8814 (mmm) cc_final: 0.8599 (tpp) REVERT: J 847 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: J 983 LYS cc_start: 0.7997 (pttm) cc_final: 0.7345 (pttm) REVERT: J 992 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7968 (mtpp) REVERT: J 1174 ARG cc_start: 0.8424 (ptt-90) cc_final: 0.8062 (ttp80) REVERT: J 1195 GLN cc_start: 0.6984 (mt0) cc_final: 0.6718 (mp10) REVERT: J 1197 ASN cc_start: 0.7624 (p0) cc_final: 0.6509 (t0) REVERT: J 1284 ARG cc_start: 0.8828 (tpp-160) cc_final: 0.8205 (tpp-160) REVERT: J 1295 ASN cc_start: 0.5717 (OUTLIER) cc_final: 0.5493 (p0) REVERT: K 11 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7206 (mp0) outliers start: 73 outliers final: 35 residues processed: 402 average time/residue: 0.3868 time to fit residues: 245.9059 Evaluate side-chains 356 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 315 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 147 GLN Chi-restraints excluded: chain I residue 97 ARG Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 1106 ARG Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 76 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 2.9990 chunk 280 optimal weight: 0.0050 chunk 61 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 ASN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 526 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27422 Z= 0.202 Angle : 0.530 12.255 37475 Z= 0.271 Chirality : 0.041 0.299 4317 Planarity : 0.004 0.047 4556 Dihedral : 15.679 176.447 4693 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.67 % Allowed : 20.27 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.15), residues: 3152 helix: 1.45 (0.16), residues: 1110 sheet: -0.64 (0.28), residues: 348 loop : -0.53 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP J 115 HIS 0.003 0.001 HIS J 430 PHE 0.040 0.001 PHE I1025 TYR 0.022 0.001 TYR I1229 ARG 0.007 0.000 ARG I 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 324 time to evaluate : 2.672 Fit side-chains revert: symmetry clash REVERT: G 141 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8563 (p) REVERT: G 176 CYS cc_start: 0.7525 (t) cc_final: 0.7058 (p) REVERT: H 84 ASN cc_start: 0.8206 (m110) cc_final: 0.7790 (m110) REVERT: H 185 TYR cc_start: 0.8530 (p90) cc_final: 0.8168 (p90) REVERT: H 197 ASP cc_start: 0.6924 (p0) cc_final: 0.6672 (p0) REVERT: I 47 TYR cc_start: 0.3248 (m-80) cc_final: 0.2310 (m-10) REVERT: I 237 LEU cc_start: 0.7123 (tt) cc_final: 0.6906 (mp) REVERT: I 423 ASP cc_start: 0.7910 (p0) cc_final: 0.7685 (p0) REVERT: I 443 ASP cc_start: 0.7720 (p0) cc_final: 0.7432 (p0) REVERT: I 496 LYS cc_start: 0.8193 (tttt) cc_final: 0.7600 (mppt) REVERT: I 766 ASN cc_start: 0.8242 (t0) cc_final: 0.8023 (t0) REVERT: I 1229 TYR cc_start: 0.8291 (m-10) cc_final: 0.8063 (m-80) REVERT: I 1233 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8670 (mt) REVERT: J 52 GLU cc_start: 0.7118 (tp30) cc_final: 0.6814 (mm-30) REVERT: J 96 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8111 (pptt) REVERT: J 129 ASP cc_start: 0.7368 (t0) cc_final: 0.6810 (t0) REVERT: J 136 GLU cc_start: 0.7745 (pp20) cc_final: 0.7515 (tp30) REVERT: J 140 TYR cc_start: 0.7810 (m-10) cc_final: 0.6940 (m-10) REVERT: J 186 GLN cc_start: 0.7693 (tt0) cc_final: 0.7386 (tt0) REVERT: J 237 MET cc_start: 0.8963 (mtt) cc_final: 0.8665 (mtt) REVERT: J 239 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8481 (pp) REVERT: J 375 GLU cc_start: 0.8279 (tp30) cc_final: 0.8022 (tp30) REVERT: J 698 MET cc_start: 0.8832 (mmm) cc_final: 0.8626 (tpp) REVERT: J 847 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: J 983 LYS cc_start: 0.7968 (pttm) cc_final: 0.7606 (pttm) REVERT: J 992 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7947 (mtpp) REVERT: J 1174 ARG cc_start: 0.8413 (ptt-90) cc_final: 0.8053 (ttp80) REVERT: J 1195 GLN cc_start: 0.7067 (mt0) cc_final: 0.6803 (mp10) REVERT: J 1197 ASN cc_start: 0.7626 (p0) cc_final: 0.6553 (t0) REVERT: J 1284 ARG cc_start: 0.8647 (tpp-160) cc_final: 0.8387 (ttm-80) REVERT: J 1295 ASN cc_start: 0.5781 (OUTLIER) cc_final: 0.5569 (p0) REVERT: K 11 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: K 72 GLN cc_start: 0.7053 (tp40) cc_final: 0.6830 (tp40) outliers start: 72 outliers final: 42 residues processed: 379 average time/residue: 0.3913 time to fit residues: 236.1497 Evaluate side-chains 355 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 307 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 0.4980 chunk 35 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 0.0000 chunk 262 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27422 Z= 0.166 Angle : 0.528 14.400 37475 Z= 0.270 Chirality : 0.040 0.245 4317 Planarity : 0.003 0.047 4556 Dihedral : 15.640 176.132 4691 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.33 % Allowed : 21.12 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3152 helix: 1.48 (0.16), residues: 1112 sheet: -0.48 (0.29), residues: 331 loop : -0.55 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP J 115 HIS 0.003 0.000 HIS G 132 PHE 0.038 0.001 PHE I1025 TYR 0.019 0.001 TYR I1229 ARG 0.004 0.000 ARG J 547 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 335 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 141 SER cc_start: 0.8843 (m) cc_final: 0.8575 (p) REVERT: G 176 CYS cc_start: 0.7509 (t) cc_final: 0.7106 (p) REVERT: H 84 ASN cc_start: 0.8136 (m110) cc_final: 0.7723 (m110) REVERT: H 185 TYR cc_start: 0.8468 (p90) cc_final: 0.8142 (p90) REVERT: H 197 ASP cc_start: 0.6899 (p0) cc_final: 0.6664 (p0) REVERT: I 237 LEU cc_start: 0.7386 (tt) cc_final: 0.7097 (mp) REVERT: I 423 ASP cc_start: 0.7902 (p0) cc_final: 0.7686 (p0) REVERT: I 443 ASP cc_start: 0.7642 (p0) cc_final: 0.7399 (p0) REVERT: I 496 LYS cc_start: 0.8193 (tttt) cc_final: 0.7601 (mppt) REVERT: I 785 ASP cc_start: 0.7605 (m-30) cc_final: 0.7370 (m-30) REVERT: I 1025 PHE cc_start: 0.6660 (m-10) cc_final: 0.6371 (m-10) REVERT: I 1233 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8637 (mt) REVERT: J 52 GLU cc_start: 0.7035 (tp30) cc_final: 0.6737 (mm-30) REVERT: J 69 GLU cc_start: 0.7712 (mp0) cc_final: 0.7316 (mp0) REVERT: J 96 LYS cc_start: 0.8314 (ptpt) cc_final: 0.8052 (pptt) REVERT: J 129 ASP cc_start: 0.7299 (t0) cc_final: 0.6774 (t0) REVERT: J 136 GLU cc_start: 0.7713 (pp20) cc_final: 0.7486 (tp30) REVERT: J 140 TYR cc_start: 0.7777 (m-10) cc_final: 0.6795 (m-10) REVERT: J 180 MET cc_start: 0.8021 (tmm) cc_final: 0.7821 (tmm) REVERT: J 186 GLN cc_start: 0.7689 (tt0) cc_final: 0.7447 (tt0) REVERT: J 237 MET cc_start: 0.8977 (mtt) cc_final: 0.8673 (mtt) REVERT: J 239 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8427 (pp) REVERT: J 375 GLU cc_start: 0.8242 (tp30) cc_final: 0.8005 (tp30) REVERT: J 698 MET cc_start: 0.8802 (mmm) cc_final: 0.8558 (tpp) REVERT: J 992 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7948 (mtpp) REVERT: J 1195 GLN cc_start: 0.7034 (mt0) cc_final: 0.6811 (mp10) REVERT: J 1197 ASN cc_start: 0.7542 (p0) cc_final: 0.6361 (t0) REVERT: J 1284 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8374 (ttm-80) REVERT: J 1295 ASN cc_start: 0.5778 (OUTLIER) cc_final: 0.5535 (p0) REVERT: K 11 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6960 (mp0) outliers start: 63 outliers final: 42 residues processed: 383 average time/residue: 0.3919 time to fit residues: 240.1957 Evaluate side-chains 356 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 310 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27422 Z= 0.254 Angle : 0.561 15.048 37475 Z= 0.286 Chirality : 0.042 0.247 4317 Planarity : 0.004 0.049 4556 Dihedral : 15.692 176.481 4691 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.45 % Allowed : 21.56 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.15), residues: 3152 helix: 1.41 (0.16), residues: 1101 sheet: -0.59 (0.27), residues: 377 loop : -0.57 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 115 HIS 0.004 0.001 HIS J 430 PHE 0.035 0.001 PHE I1025 TYR 0.025 0.001 TYR I1229 ARG 0.008 0.000 ARG J1174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 335 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8445 (m-80) cc_final: 0.7823 (t80) REVERT: H 60 GLU cc_start: 0.7025 (pm20) cc_final: 0.6750 (pm20) REVERT: H 84 ASN cc_start: 0.8284 (m110) cc_final: 0.7865 (m110) REVERT: H 185 TYR cc_start: 0.8569 (p90) cc_final: 0.8200 (p90) REVERT: H 194 GLN cc_start: 0.8206 (tp40) cc_final: 0.7958 (tp40) REVERT: I 47 TYR cc_start: 0.3520 (m-80) cc_final: 0.2573 (m-80) REVERT: I 214 ASN cc_start: 0.8688 (t0) cc_final: 0.8404 (t0) REVERT: I 237 LEU cc_start: 0.7482 (tt) cc_final: 0.7174 (mp) REVERT: I 443 ASP cc_start: 0.7760 (p0) cc_final: 0.7498 (p0) REVERT: I 496 LYS cc_start: 0.8253 (tttt) cc_final: 0.7632 (mppt) REVERT: I 1188 ASP cc_start: 0.8737 (p0) cc_final: 0.8317 (p0) REVERT: I 1233 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8678 (mt) REVERT: J 52 GLU cc_start: 0.7096 (tp30) cc_final: 0.6862 (mm-30) REVERT: J 69 GLU cc_start: 0.7749 (mp0) cc_final: 0.7408 (mp0) REVERT: J 96 LYS cc_start: 0.8346 (ptpt) cc_final: 0.8118 (pptt) REVERT: J 129 ASP cc_start: 0.7435 (t0) cc_final: 0.6919 (t0) REVERT: J 140 TYR cc_start: 0.7964 (m-10) cc_final: 0.6952 (m-10) REVERT: J 186 GLN cc_start: 0.7782 (tt0) cc_final: 0.7536 (tt0) REVERT: J 237 MET cc_start: 0.9047 (mtt) cc_final: 0.8756 (mtt) REVERT: J 239 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8509 (pp) REVERT: J 375 GLU cc_start: 0.8307 (tp30) cc_final: 0.8054 (tp30) REVERT: J 457 TYR cc_start: 0.8486 (m-80) cc_final: 0.8254 (m-80) REVERT: J 698 MET cc_start: 0.8828 (mmm) cc_final: 0.8626 (tpp) REVERT: J 992 LYS cc_start: 0.8383 (mmmt) cc_final: 0.7881 (mtpp) REVERT: J 1195 GLN cc_start: 0.7174 (mt0) cc_final: 0.6936 (mp10) REVERT: J 1197 ASN cc_start: 0.7586 (p0) cc_final: 0.6358 (t0) REVERT: J 1284 ARG cc_start: 0.8623 (tpp-160) cc_final: 0.8336 (ttm-80) REVERT: J 1295 ASN cc_start: 0.5868 (OUTLIER) cc_final: 0.5584 (p0) REVERT: K 11 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6958 (mp0) outliers start: 66 outliers final: 48 residues processed: 385 average time/residue: 0.3687 time to fit residues: 228.3514 Evaluate side-chains 363 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 311 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 130 MET Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 684 ASP Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.9980 chunk 271 optimal weight: 20.0000 chunk 289 optimal weight: 0.3980 chunk 174 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27422 Z= 0.183 Angle : 0.547 15.447 37475 Z= 0.279 Chirality : 0.041 0.240 4317 Planarity : 0.004 0.053 4556 Dihedral : 15.655 176.090 4691 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.30 % Allowed : 22.42 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.15), residues: 3152 helix: 1.45 (0.16), residues: 1109 sheet: -0.56 (0.28), residues: 360 loop : -0.60 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP J 115 HIS 0.003 0.001 HIS G 132 PHE 0.036 0.001 PHE I1025 TYR 0.020 0.001 TYR I1229 ARG 0.004 0.000 ARG J1174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 327 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8290 (m-80) cc_final: 0.7792 (t80) REVERT: G 176 CYS cc_start: 0.7684 (t) cc_final: 0.7160 (p) REVERT: H 60 GLU cc_start: 0.7037 (pm20) cc_final: 0.6763 (pm20) REVERT: H 84 ASN cc_start: 0.8254 (m110) cc_final: 0.7820 (m110) REVERT: H 185 TYR cc_start: 0.8553 (p90) cc_final: 0.8216 (p90) REVERT: H 194 GLN cc_start: 0.8185 (tp40) cc_final: 0.7946 (tp40) REVERT: I 214 ASN cc_start: 0.8667 (t0) cc_final: 0.8364 (t0) REVERT: I 237 LEU cc_start: 0.7539 (tt) cc_final: 0.7260 (mp) REVERT: I 443 ASP cc_start: 0.7679 (p0) cc_final: 0.7434 (p0) REVERT: I 496 LYS cc_start: 0.8249 (tttt) cc_final: 0.7634 (mppt) REVERT: I 785 ASP cc_start: 0.7625 (m-30) cc_final: 0.7387 (m-30) REVERT: I 1188 ASP cc_start: 0.8702 (p0) cc_final: 0.8401 (p0) REVERT: I 1233 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8609 (mt) REVERT: I 1279 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7682 (mt-10) REVERT: J 52 GLU cc_start: 0.7064 (tp30) cc_final: 0.6814 (mm-30) REVERT: J 53 ARG cc_start: 0.8165 (tmt170) cc_final: 0.7803 (tpt90) REVERT: J 69 GLU cc_start: 0.7752 (mp0) cc_final: 0.7392 (mp0) REVERT: J 96 LYS cc_start: 0.8334 (ptpt) cc_final: 0.8100 (pptt) REVERT: J 129 ASP cc_start: 0.7327 (t0) cc_final: 0.6796 (t0) REVERT: J 186 GLN cc_start: 0.7732 (tt0) cc_final: 0.7485 (tt0) REVERT: J 237 MET cc_start: 0.9033 (mtt) cc_final: 0.8741 (mtt) REVERT: J 239 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8426 (pp) REVERT: J 312 ARG cc_start: 0.5963 (mmm160) cc_final: 0.5727 (mmm160) REVERT: J 375 GLU cc_start: 0.8271 (tp30) cc_final: 0.8057 (tp30) REVERT: J 698 MET cc_start: 0.8807 (mmm) cc_final: 0.8569 (tpp) REVERT: J 706 VAL cc_start: 0.8132 (t) cc_final: 0.7920 (p) REVERT: J 992 LYS cc_start: 0.8440 (mmmt) cc_final: 0.7944 (mtpp) REVERT: J 1174 ARG cc_start: 0.8299 (ttp80) cc_final: 0.8090 (ttp80) REVERT: J 1197 ASN cc_start: 0.7584 (p0) cc_final: 0.6328 (t0) REVERT: J 1284 ARG cc_start: 0.8633 (tpp-160) cc_final: 0.8331 (ttm-80) REVERT: J 1295 ASN cc_start: 0.5828 (OUTLIER) cc_final: 0.5559 (p0) REVERT: K 11 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6927 (mp0) outliers start: 62 outliers final: 49 residues processed: 377 average time/residue: 0.3826 time to fit residues: 234.3513 Evaluate side-chains 367 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 314 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 320 optimal weight: 40.0000 chunk 295 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27422 Z= 0.239 Angle : 0.572 14.656 37475 Z= 0.291 Chirality : 0.042 0.255 4317 Planarity : 0.004 0.052 4556 Dihedral : 15.675 176.321 4691 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.26 % Allowed : 22.60 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.15), residues: 3152 helix: 1.41 (0.16), residues: 1103 sheet: -0.45 (0.27), residues: 372 loop : -0.62 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 115 HIS 0.004 0.001 HIS J 430 PHE 0.035 0.001 PHE I1025 TYR 0.022 0.001 TYR I1229 ARG 0.004 0.000 ARG J 731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 318 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8337 (m-80) cc_final: 0.7785 (t80) REVERT: H 60 GLU cc_start: 0.7014 (pm20) cc_final: 0.6736 (pm20) REVERT: H 84 ASN cc_start: 0.8278 (m110) cc_final: 0.7847 (m110) REVERT: H 185 TYR cc_start: 0.8615 (p90) cc_final: 0.8275 (p90) REVERT: H 194 GLN cc_start: 0.8192 (tp40) cc_final: 0.7937 (tp40) REVERT: I 47 TYR cc_start: 0.3351 (m-80) cc_final: 0.2593 (m-80) REVERT: I 214 ASN cc_start: 0.8646 (t0) cc_final: 0.8297 (t0) REVERT: I 237 LEU cc_start: 0.7533 (tt) cc_final: 0.7245 (mp) REVERT: I 443 ASP cc_start: 0.7731 (p0) cc_final: 0.7484 (p0) REVERT: I 496 LYS cc_start: 0.8206 (tttt) cc_final: 0.7570 (mppt) REVERT: I 1188 ASP cc_start: 0.8773 (p0) cc_final: 0.8459 (p0) REVERT: I 1233 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8658 (mt) REVERT: J 69 GLU cc_start: 0.7753 (mp0) cc_final: 0.7417 (mp0) REVERT: J 96 LYS cc_start: 0.8362 (ptpt) cc_final: 0.8159 (pptt) REVERT: J 129 ASP cc_start: 0.7306 (t0) cc_final: 0.6784 (t0) REVERT: J 136 GLU cc_start: 0.7997 (tp30) cc_final: 0.7014 (tp30) REVERT: J 186 GLN cc_start: 0.7775 (tt0) cc_final: 0.7525 (tt0) REVERT: J 237 MET cc_start: 0.9051 (mtt) cc_final: 0.8756 (mtt) REVERT: J 239 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8453 (pp) REVERT: J 375 GLU cc_start: 0.8279 (tp30) cc_final: 0.8072 (tp30) REVERT: J 457 TYR cc_start: 0.8466 (m-80) cc_final: 0.8201 (m-80) REVERT: J 698 MET cc_start: 0.8809 (mmm) cc_final: 0.8591 (tpp) REVERT: J 706 VAL cc_start: 0.8178 (t) cc_final: 0.7970 (p) REVERT: J 992 LYS cc_start: 0.8414 (mmmt) cc_final: 0.7899 (mtpp) REVERT: J 1172 LYS cc_start: 0.7326 (tptp) cc_final: 0.7015 (tptp) REVERT: J 1174 ARG cc_start: 0.8278 (ttp80) cc_final: 0.8064 (ttp80) REVERT: J 1197 ASN cc_start: 0.7672 (p0) cc_final: 0.6352 (t0) REVERT: J 1284 ARG cc_start: 0.8636 (tpp-160) cc_final: 0.8351 (ttm-80) REVERT: J 1295 ASN cc_start: 0.5825 (OUTLIER) cc_final: 0.5558 (p0) REVERT: K 11 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6896 (mp0) outliers start: 61 outliers final: 54 residues processed: 367 average time/residue: 0.3857 time to fit residues: 228.7126 Evaluate side-chains 370 residues out of total 2701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 312 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 620 ASN Chi-restraints excluded: chain I residue 681 MET Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 844 LYS Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 927 THR Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 992 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1259 LEU Chi-restraints excluded: chain I residue 1291 LEU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 239 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 279 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 602 SER Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 875 ASN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1295 ASN Chi-restraints excluded: chain J residue 1313 SER Chi-restraints excluded: chain J residue 1329 THR Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 224 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 69 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101451 restraints weight = 42272.796| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.57 r_work: 0.3113 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27422 Z= 0.317 Angle : 0.615 15.178 37475 Z= 0.315 Chirality : 0.043 0.292 4317 Planarity : 0.004 0.064 4556 Dihedral : 15.751 176.178 4691 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.41 % Allowed : 22.82 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.15), residues: 3152 helix: 1.25 (0.16), residues: 1104 sheet: -0.61 (0.28), residues: 361 loop : -0.65 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 115 HIS 0.005 0.001 HIS J 430 PHE 0.032 0.002 PHE I1025 TYR 0.026 0.001 TYR I1229 ARG 0.006 0.000 ARG J 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5995.75 seconds wall clock time: 108 minutes 42.12 seconds (6522.12 seconds total)